data_EMD-14544
# 
_entry.id   EMD-14544 
# 
_audit_conform.dict_name       mmcif_pdbx.dic 
_audit_conform.dict_version    5.398 
_audit_conform.dict_location   http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 
# 
loop_
_database_2.database_id 
_database_2.database_code 
_database_2.pdbx_database_accession 
_database_2.pdbx_DOI 
PDB   7Z86         pdb_00007z86 10.2210/pdb7z86/pdb 
WWPDB D_1292121750 ?            ?                   
EMDB  EMD-14544    ?            ?                   
# 
loop_
_pdbx_database_related.db_name 
_pdbx_database_related.details 
_pdbx_database_related.db_id 
_pdbx_database_related.content_type 
PDB  .                                                                                                     7Z85      unspecified 
PDB  .                                                                                                     7Z6V      unspecified 
PDB  .                                                                                                     7Z7X      unspecified 
EMDB 'CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-H4 Q98R H100E nanobody complex in 1Up2Down conformation' EMD-14544 
'associated EM volume' 
# 
_citation.abstract                  ? 
_citation.abstract_id_CAS           ? 
_citation.book_id_ISBN              ? 
_citation.book_publisher            ? 
_citation.book_publisher_city       ? 
_citation.book_title                ? 
_citation.coordinate_linkage        ? 
_citation.country                   US 
_citation.database_id_Medline       ? 
_citation.details                   ? 
_citation.id                        primary 
_citation.journal_abbrev            Proc.Natl.Acad.Sci.USA 
_citation.journal_id_ASTM           PNASA6 
_citation.journal_id_CSD            0040 
_citation.journal_id_ISSN           1091-6490 
_citation.journal_full              ? 
_citation.journal_issue             ? 
_citation.journal_volume            119 
_citation.language                  ? 
_citation.page_first                e2205412119 
_citation.page_last                 e2205412119 
_citation.title                     
'Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes.' 
_citation.year                      2022 
_citation.database_id_CSD           ? 
_citation.pdbx_database_id_DOI      10.1073/pnas.2205412119 
_citation.pdbx_database_id_PubMed   35858383 
_citation.pdbx_database_id_patent   ? 
_citation.unpublished_flag          ? 
# 
loop_
_citation_author.citation_id 
_citation_author.name 
_citation_author.ordinal 
_citation_author.identifier_ORCID 
primary 'Mikolajek, H.'   1  0000-0003-0776-9974 
primary 'Weckener, M.'    2  0000-0002-1419-9378 
primary 'Brotzakis, Z.F.' 3  ?                   
primary 'Huo, J.'         4  ?                   
primary 'Dalietou, E.V.'  5  ?                   
primary 'Le Bas, A.'      6  ?                   
primary 'Sormanni, P.'    7  0000-0002-6228-2221 
primary 'Harrison, P.J.'  8  ?                   
primary 'Ward, P.N.'      9  0000-0003-2546-3426 
primary 'Truong, S.'      10 0000-0001-9624-4461 
primary 'Moynie, L.'      11 0000-0002-4097-4331 
primary 'Clare, D.K.'     12 ?                   
primary 'Dumoux, M.'      13 ?                   
primary 'Dormon, J.'      14 ?                   
primary 'Norman, C.'      15 ?                   
primary 'Hussain, N.'     16 0000-0002-5170-0061 
primary 'Vogirala, V.'    17 0000-0002-8534-3736 
primary 'Owens, R.J.'     18 0000-0002-3705-2993 
primary 'Vendruscolo, M.' 19 0000-0002-3616-1610 
primary 'Naismith, J.H.'  20 0000-0001-6744-5061 
# 
loop_
_entity.id 
_entity.type 
_entity.src_method 
_entity.pdbx_description 
_entity.formula_weight 
_entity.pdbx_number_of_molecules 
_entity.pdbx_ec 
_entity.pdbx_mutation 
_entity.pdbx_fragment 
_entity.details 
1 polymer     man 'Spike glycoprotein,Fibritin'                                                             139877.906 3  ? ? ? ? 
2 polymer     man 'Nanobody H11-H4 Q98R H100E'                                                              14107.723  3  ? ? ? ? 
3 branched    man '2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose' 424.401    20 ? ? ? ? 
4 non-polymer syn 2-acetamido-2-deoxy-beta-D-glucopyranose                                                  221.208    26 ? ? ? ? 
# 
loop_
_entity_poly.entity_id 
_entity_poly.type 
_entity_poly.pdbx_seq_one_letter_code 
1 'polypeptide(L)' 
;MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFD
NPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVY
SSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT
LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRV
QPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSF
VIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC
NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFL
PFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGS
NVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI
SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGF
NFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAG
TITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALN
TLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRV
DFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNT
FVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL
QELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLSLLNDIFEAQKIEWHEKHHHHHH
;
2 'polypeptide(L)' 
;QVQLVESGGGLMQAGGSLRLSCAVSGRTFSTAAMGWFRQAPGKEREFVAAIRWSGGSAYYADSVKGRFTISRDKAKNTVY
LQMNSLKYEDTAVYYCARTEYVSYLLSDYATWPYDYWGQGTQVTVSS
;
# 
_pdbx_entity_nonpoly.entity_id   4 
_pdbx_entity_nonpoly.name        2-acetamido-2-deoxy-beta-D-glucopyranose 
_pdbx_entity_nonpoly.comp_id     NAG 
# 
loop_
_entity_src_gen.entity_id 
_entity_src_gen.pdbx_src_id 
_entity_src_gen.pdbx_alt_source_flag 
_entity_src_gen.pdbx_seq_type 
_entity_src_gen.pdbx_beg_seq_num 
_entity_src_gen.pdbx_end_seq_num 
_entity_src_gen.gene_src_common_name 
_entity_src_gen.gene_src_genus 
_entity_src_gen.pdbx_gene_src_gene 
_entity_src_gen.gene_src_species 
_entity_src_gen.gene_src_strain 
_entity_src_gen.gene_src_tissue 
_entity_src_gen.gene_src_tissue_fraction 
_entity_src_gen.gene_src_details 
_entity_src_gen.pdbx_gene_src_fragment 
_entity_src_gen.pdbx_gene_src_scientific_name 
_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 
_entity_src_gen.pdbx_gene_src_variant 
_entity_src_gen.pdbx_gene_src_cell_line 
_entity_src_gen.pdbx_gene_src_atcc 
_entity_src_gen.pdbx_gene_src_culture_collection 
_entity_src_gen.pdbx_gene_src_organ 
_entity_src_gen.pdbx_gene_src_organelle 
_entity_src_gen.pdbx_gene_src_cell 
_entity_src_gen.pdbx_gene_src_cellular_location 
_entity_src_gen.host_org_common_name 
_entity_src_gen.pdbx_host_org_scientific_name 
_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 
_entity_src_gen.host_org_genus 
_entity_src_gen.pdbx_host_org_gene 
_entity_src_gen.pdbx_host_org_organ 
_entity_src_gen.host_org_species 
_entity_src_gen.pdbx_host_org_tissue 
_entity_src_gen.pdbx_host_org_tissue_fraction 
_entity_src_gen.pdbx_host_org_strain 
_entity_src_gen.pdbx_host_org_variant 
_entity_src_gen.pdbx_host_org_cell_line 
_entity_src_gen.pdbx_host_org_atcc 
_entity_src_gen.pdbx_host_org_culture_collection 
_entity_src_gen.pdbx_host_org_cell 
_entity_src_gen.pdbx_host_org_organelle 
_entity_src_gen.pdbx_host_org_cellular_location 
_entity_src_gen.pdbx_host_org_vector_type 
_entity_src_gen.pdbx_host_org_vector 
_entity_src_gen.host_org_details 
_entity_src_gen.expression_system_id 
_entity_src_gen.plasmid_name 
_entity_src_gen.plasmid_details 
_entity_src_gen.pdbx_description 
1 1 sample 'Biological sequence' 1    1208 ? ? 'S, 2' ? ? ? ? ? ? 'Severe acute respiratory syndrome coronavirus 2' 2697049 ? ? ? 
? ? ? ? ? ? 'Homo sapiens'     9606 ? ? ? ? ? ? ?   ? 'HEK 293T Lenti-X' ? ? ? ? ? ? ? ? ? ? ? ? 
1 2 sample 'Biological sequence' 1209 1260 ? ? wac    ? ? ? ? ? ? 'Escherichia virus T4'                            10665   ? ? ? 
? ? ? ? ? ? 'Homo sapiens'     9606 ? ? ? ? ? ? ?   ? 'HEK 293T Lenti-X' ? ? ? ? ? ? ? ? ? ? ? ? 
2 1 sample 'Biological sequence' 1    127  ? ? ?      ? ? ? ? ? ? 'Lama glama'                                      9844    ? ? ? 
? ? ? ? ? ? 'Escherichia coli' 562  ? ? ? ? ? ? WK6 ? ?                  ? ? ? ? ? ? ? ? ? ? ? ? 
# 
loop_
_chem_comp.id 
_chem_comp.type 
_chem_comp.mon_nstd_flag 
_chem_comp.name 
_chem_comp.pdbx_synonyms 
_chem_comp.formula 
_chem_comp.formula_weight 
ALA 'L-peptide linking'          y ALANINE                                  ? 'C3 H7 N O2'     89.093  
ARG 'L-peptide linking'          y ARGININE                                 ? 'C6 H15 N4 O2 1' 175.209 
ASN 'L-peptide linking'          y ASPARAGINE                               ? 'C4 H8 N2 O3'    132.118 
ASP 'L-peptide linking'          y 'ASPARTIC ACID'                          ? 'C4 H7 N O4'     133.103 
CYS 'L-peptide linking'          y CYSTEINE                                 ? 'C3 H7 N O2 S'   121.158 
GLN 'L-peptide linking'          y GLUTAMINE                                ? 'C5 H10 N2 O3'   146.144 
GLU 'L-peptide linking'          y 'GLUTAMIC ACID'                          ? 'C5 H9 N O4'     147.129 
GLY 'peptide linking'            y GLYCINE                                  ? 'C2 H5 N O2'     75.067  
HIS 'L-peptide linking'          y HISTIDINE                                ? 'C6 H10 N3 O2 1' 156.162 
ILE 'L-peptide linking'          y ISOLEUCINE                               ? 'C6 H13 N O2'    131.173 
LEU 'L-peptide linking'          y LEUCINE                                  ? 'C6 H13 N O2'    131.173 
LYS 'L-peptide linking'          y LYSINE                                   ? 'C6 H15 N2 O2 1' 147.195 
MET 'L-peptide linking'          y METHIONINE                               ? 'C5 H11 N O2 S'  149.211 
NAG 'D-saccharide, beta linking' . 2-acetamido-2-deoxy-beta-D-glucopyranose 
;N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE
;
'C8 H15 N O6'    221.208 
PHE 'L-peptide linking'          y PHENYLALANINE                            ? 'C9 H11 N O2'    165.189 
PRO 'L-peptide linking'          y PROLINE                                  ? 'C5 H9 N O2'     115.130 
SER 'L-peptide linking'          y SERINE                                   ? 'C3 H7 N O3'     105.093 
THR 'L-peptide linking'          y THREONINE                                ? 'C4 H9 N O3'     119.119 
TRP 'L-peptide linking'          y TRYPTOPHAN                               ? 'C11 H12 N2 O2'  204.225 
TYR 'L-peptide linking'          y TYROSINE                                 ? 'C9 H11 N O3'    181.189 
VAL 'L-peptide linking'          y VALINE                                   ? 'C5 H11 N O2'    117.146 
# 
_exptl.entry_id         EMD-14544 
_exptl.details          ? 
_exptl.method           'ELECTRON MICROSCOPY' 
_exptl.method_details   ? 
# 
_struct_keywords.entry_id        EMD-14544 
_struct_keywords.text            'Complex, Spike glycoprotein, nanobody H11-H4 Q98R H100E, ANTIVIRAL PROTEIN' 
_struct_keywords.pdbx_keywords   'ANTIVIRAL PROTEIN' 
_struct_keywords.pdbx_details    ? 
# 
loop_
_struct_ref.id 
_struct_ref.db_name 
_struct_ref.db_code 
_struct_ref.entity_id 
1 UNP SPIKE_SARS2 1 
2 UNP WAC_BPT4    1 
3 PDB 7Z86        2 
# 
_em_3d_fitting.entry_id          EMD-14544 
_em_3d_fitting.id                1 
_em_3d_fitting.details           ? 
_em_3d_fitting.overall_b_value   ? 
_em_3d_fitting.ref_protocol      'RIGID BODY FIT' 
_em_3d_fitting.ref_space         RECIPROCAL 
_em_3d_fitting.target_criteria   ? 
_em_3d_fitting.method            ? 
# 
loop_
_em_3d_fitting_list.3d_fitting_id 
_em_3d_fitting_list.id 
_em_3d_fitting_list.details 
_em_3d_fitting_list.pdb_chain_id 
_em_3d_fitting_list.pdb_chain_residue_range 
_em_3d_fitting_list.pdb_entry_id 
_em_3d_fitting_list.initial_refinement_model_id 
_em_3d_fitting_list.chain_id 
_em_3d_fitting_list.chain_residue_range 
_em_3d_fitting_list.source_name 
_em_3d_fitting_list.type 
_em_3d_fitting_list.accession_code 
1 1 ? A 27-1147 6ZHD 1 ? ? PDB 'experimental model' 6ZHD 
1 2 ? B 27-1147 6ZHD 1 ? ? PDB 'experimental model' 6ZHD 
1 3 ? C 27-1147 6ZHD 1 ? ? PDB 'experimental model' 6ZHD 
# 
_em_3d_reconstruction.entry_id                    EMD-14544 
_em_3d_reconstruction.id                          1 
_em_3d_reconstruction.algorithm                   ? 
_em_3d_reconstruction.details                     ? 
_em_3d_reconstruction.fsc_type                    'EVEN/ODD MAPS REFINED TOTALLY INDEPENDENT (GOLD STANDARD)' 
_em_3d_reconstruction.refinement_type             ? 
_em_3d_reconstruction.image_processing_id         1 
_em_3d_reconstruction.num_class_averages          1 
_em_3d_reconstruction.num_particles               396910 
_em_3d_reconstruction.resolution                  3.4 
_em_3d_reconstruction.resolution_method           'FSC 0.143 CUT-OFF' 
_em_3d_reconstruction.symmetry_type               POINT 
_em_3d_reconstruction.method                      ? 
_em_3d_reconstruction.nominal_pixel_size          ? 
_em_3d_reconstruction.actual_pixel_size           ? 
_em_3d_reconstruction.magnification_calibration   ? 
# 
_em_buffer.id            1 
_em_buffer.details       ? 
_em_buffer.pH            8 
_em_buffer.specimen_id   1 
_em_buffer.name          ? 
# 
loop_
_em_entity_assembly.id 
_em_entity_assembly.parent_id 
_em_entity_assembly.details 
_em_entity_assembly.go_id 
_em_entity_assembly.name 
_em_entity_assembly.source 
_em_entity_assembly.type 
_em_entity_assembly.chimera 
_em_entity_assembly.entity_id_list 
_em_entity_assembly.ipr_id 
_em_entity_assembly.synonym 
_em_entity_assembly.number_of_copies 
_em_entity_assembly.oligomeric_details 
1 0 ? ? 'Complex between Spike and nanobody H11-H4 Q98R H100E' 'MULTIPLE SOURCES' COMPLEX NO  '1, 2' ? ? ? ? 
2 1 ? ? 'Spike glycoprotein trimer with fibritin tag'          RECOMBINANT        COMPLEX YES 1      ? ? ? ? 
3 1 ? ? 'Nanobody H11-H4 Q98R H100E'                           RECOMBINANT        COMPLEX NO  2      ? ? ? ? 
# 
_em_image_scans.entry_id                EMD-14544 
_em_image_scans.id                      1 
_em_image_scans.dimension_height        4092 
_em_image_scans.dimension_width         5760 
_em_image_scans.frames_per_image        ? 
_em_image_scans.image_recording_id      1 
_em_image_scans.sampling_size           ? 
_em_image_scans.scanner_model           ? 
_em_image_scans.used_frames_per_image   ? 
_em_image_scans.citation_id             ? 
_em_image_scans.number_digital_images   ? 
_em_image_scans.od_range                ? 
_em_image_scans.quant_bit_size          ? 
_em_image_scans.details                 ? 
# 
_em_imaging.id                              1 
_em_imaging.entry_id                        EMD-14544 
_em_imaging.accelerating_voltage            300 
_em_imaging.alignment_procedure             'ZEMLIN TABLEAU' 
_em_imaging.c2_aperture_diameter            70 
_em_imaging.calibrated_defocus_max          ? 
_em_imaging.calibrated_defocus_min          ? 
_em_imaging.calibrated_magnification        ? 
_em_imaging.cryogen                         NITROGEN 
_em_imaging.details                         'EPU auto-function coma free correction' 
_em_imaging.electron_source                 'FIELD EMISSION GUN' 
_em_imaging.illumination_mode               'FLOOD BEAM' 
_em_imaging.microscope_model                'TFS KRIOS' 
_em_imaging.mode                            'BRIGHT FIELD' 
_em_imaging.nominal_cs                      2.7 
_em_imaging.nominal_defocus_max             3000 
_em_imaging.nominal_defocus_min             1500 
_em_imaging.nominal_magnification           81000 
_em_imaging.recording_temperature_maximum   ? 
_em_imaging.recording_temperature_minimum   ? 
_em_imaging.residual_tilt                   ? 
_em_imaging.specimen_holder_model           'FEI TITAN KRIOS AUTOGRID HOLDER' 
_em_imaging.specimen_id                     1 
_em_imaging.sample_support_id               1 
_em_imaging.citation_id                     ? 
_em_imaging.detector_id                     1 
_em_imaging.scans_id                        1 
_em_imaging.date                            ? 
_em_imaging.temperature                     ? 
_em_imaging.tilt_angle_min                  ? 
_em_imaging.tilt_angle_max                  ? 
_em_imaging.astigmatism                     ? 
_em_imaging.detector_distance               ? 
_em_imaging.electron_beam_tilt_params       ? 
_em_imaging.specimen_holder_type            ? 
# 
_em_sample_support.id               1 
_em_sample_support.specimen_id      1 
_em_sample_support.details          'Grids were glow discharged twice, 60 s each time.' 
_em_sample_support.grid_material    GOLD 
_em_sample_support.grid_mesh_size   200 
_em_sample_support.grid_type        'Quantifoil R1.2/1.3' 
_em_sample_support.method           ? 
_em_sample_support.film_material    ? 
# 
_em_vitrification.id                      1 
_em_vitrification.specimen_id             1 
_em_vitrification.chamber_temperature     ? 
_em_vitrification.cryogen_name            ETHANE 
_em_vitrification.details                 ? 
_em_vitrification.humidity                ? 
_em_vitrification.instrument              'FEI VITROBOT MARK IV' 
_em_vitrification.entry_id                EMD-14544 
_em_vitrification.sample_preparation_id   ? 
_em_vitrification.citation_id             ? 
_em_vitrification.method                  ? 
_em_vitrification.temp                    ? 
_em_vitrification.time_resolved_state     ? 
# 
_em_experiment.entry_id                EMD-14544 
_em_experiment.id                      1 
_em_experiment.aggregation_state       PARTICLE 
_em_experiment.reconstruction_method   'SINGLE PARTICLE' 
_em_experiment.entity_assembly_id      1 
# 
_em_single_particle_entity.entry_id              EMD-14544 
_em_single_particle_entity.id                    1 
_em_single_particle_entity.image_processing_id   1 
_em_single_particle_entity.point_symmetry        C1 
# 
_em_admin.entry_id              EMD-14544 
_em_admin.current_status        REL 
_em_admin.deposition_date       2022-03-16 
_em_admin.deposition_site       PDBE 
_em_admin.details               ? 
_em_admin.last_update           2024-11-13 
_em_admin.map_release_date      2022-07-13 
_em_admin.obsoleted_date        ? 
_em_admin.title                 
'CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-H4 Q98R H100E nanobody complex in 1Up2Down conformation' 
_em_admin.header_release_date   2022-07-13 
# 
loop_
_em_author_list.ordinal 
_em_author_list.author 
_em_author_list.identifier_ORCID 
1 'Weckener, M.'   ? 
2 'Naismith, J.H.' ? 
3 'Vogirala, V.K.' ? 
# 
loop_
_em_buffer_component.buffer_id 
_em_buffer_component.id 
_em_buffer_component.concentration 
_em_buffer_component.concentration_units 
_em_buffer_component.formula 
_em_buffer_component.name 
1 1 10  mM HEPES HEPES             
1 2 150 mM NaCl  'Sodium chloride' 
# 
_em_ctf_correction.id                                1 
_em_ctf_correction.em_image_processing_id            1 
_em_ctf_correction.type                              'PHASE FLIPPING AND AMPLITUDE CORRECTION' 
_em_ctf_correction.details                           ? 
_em_ctf_correction.amplitude_correction              ? 
_em_ctf_correction.amplitude_correction_factor       ? 
_em_ctf_correction.amplitude_correction_space        ? 
_em_ctf_correction.correction_operation              ? 
_em_ctf_correction.phase_reversal                    ? 
_em_ctf_correction.phase_reversal_anisotropic        ? 
_em_ctf_correction.phase_reversal_correction_space   ? 
# 
_em_db_reference.id             1 
_em_db_reference.access_code    7Z86 
_em_db_reference.db_name        PDB 
_em_db_reference.details        ? 
_em_db_reference.relationship   'IN FRAME' 
# 
loop_
_em_entity_assembly_molwt.entity_assembly_id 
_em_entity_assembly_molwt.id 
_em_entity_assembly_molwt.experimental_flag 
_em_entity_assembly_molwt.units 
_em_entity_assembly_molwt.value 
1 1 NO MEGADALTONS 0.52  
1 2 NO MEGADALTONS 0.142 
1 3 NO MEGADALTONS 0.015 
# 
loop_
_em_entity_assembly_naturalsource.id 
_em_entity_assembly_naturalsource.entity_assembly_id 
_em_entity_assembly_naturalsource.cell 
_em_entity_assembly_naturalsource.cellular_location 
_em_entity_assembly_naturalsource.ncbi_tax_id 
_em_entity_assembly_naturalsource.organ 
_em_entity_assembly_naturalsource.organelle 
_em_entity_assembly_naturalsource.organism 
_em_entity_assembly_naturalsource.strain 
_em_entity_assembly_naturalsource.tissue 
2 2 ? ? 2697049 ? ? 'Severe acute respiratory syndrome coronavirus 2' ? ? 
3 2 ? ? 10665   ? ? 'Escherichia virus T4'                            ? ? 
4 3 ? ? 9844    ? ? 'Lama glama'                                      ? ? 
# 
loop_
_em_entity_assembly_recombinant.id 
_em_entity_assembly_recombinant.entity_assembly_id 
_em_entity_assembly_recombinant.cell 
_em_entity_assembly_recombinant.ncbi_tax_id 
_em_entity_assembly_recombinant.organism 
_em_entity_assembly_recombinant.plasmid 
_em_entity_assembly_recombinant.strain 
2 2 ? 9606 'Homo sapiens'     ? 'HEK 293T' 
3 2 ? 9606 'Homo sapiens'     ? 'HEK 293T' 
4 3 ? 562  'Escherichia coli' ? WK6        
# 
loop_
_em_euler_angle_assignment.id 
_em_euler_angle_assignment.details 
_em_euler_angle_assignment.image_processing_id 
_em_euler_angle_assignment.order 
_em_euler_angle_assignment.proj_matching_angular_sampling 
_em_euler_angle_assignment.proj_matching_merit_function 
_em_euler_angle_assignment.proj_matching_num_projections 
_em_euler_angle_assignment.type 
1 ? 1 INITIAL ? ? ? 'MAXIMUM LIKELIHOOD' 
2 ? 1 FINAL   ? ? ? 'MAXIMUM LIKELIHOOD' 
# 
_em_final_classification.id                         1 
_em_final_classification.type                       3D 
_em_final_classification.avg_num_images_per_class   ? 
_em_final_classification.details                    ? 
_em_final_classification.image_processing_id        1 
_em_final_classification.num_classes                3 
# 
_em_grid_pretreatment.id                  1 
_em_grid_pretreatment.sample_support_id   1 
_em_grid_pretreatment.atmosphere          Air 
_em_grid_pretreatment.pressure            ? 
_em_grid_pretreatment.time                120 
_em_grid_pretreatment.type                'GLOW DISCHARGE' 
# 
_em_image_processing.id                   1 
_em_image_processing.image_recording_id   1 
_em_image_processing.details              ? 
# 
_em_image_recording.id                                  1 
_em_image_recording.imaging_id                          1 
_em_image_recording.avg_electron_dose_per_image         50 
_em_image_recording.average_exposure_time               3.85 
_em_image_recording.details                             'The images were collected as 50 frame movies' 
_em_image_recording.detector_mode                       ? 
_em_image_recording.film_or_detector_model              'GATAN K3 BIOQUANTUM (6k x 4k)' 
_em_image_recording.num_diffraction_images              ? 
_em_image_recording.num_grids_imaged                    1 
_em_image_recording.num_real_images                     ? 
_em_image_recording.avg_electron_dose_per_subtomogram   ? 
# 
_em_imaging_optics.id                         1 
_em_imaging_optics.imaging_id                 1 
_em_imaging_optics.chr_aberration_corrector   ? 
_em_imaging_optics.energyfilter_lower         ? 
_em_imaging_optics.energyfilter_name          'GIF Quantum LS' 
_em_imaging_optics.energyfilter_upper         ? 
_em_imaging_optics.energyfilter_slit_width    20 
_em_imaging_optics.phase_plate                ? 
_em_imaging_optics.sph_aberration_corrector   ? 
_em_imaging_optics.details                    ? 
# 
loop_
_em_map.entry_id 
_em_map.id 
_em_map.annotation_details 
_em_map.axis_order_fast 
_em_map.axis_order_medium 
_em_map.axis_order_slow 
_em_map.cell_a 
_em_map.cell_alpha 
_em_map.cell_b 
_em_map.cell_beta 
_em_map.cell_c 
_em_map.cell_gamma 
_em_map.contour_level 
_em_map.contour_level_source 
_em_map.data_type 
_em_map.dimensions_col 
_em_map.dimensions_row 
_em_map.dimensions_sec 
_em_map.endian_type 
_em_map.file 
_em_map.format 
_em_map.label 
_em_map.limit_col 
_em_map.limit_row 
_em_map.limit_sec 
_em_map.origin_col 
_em_map.origin_row 
_em_map.origin_sec 
_em_map.partition 
_em_map.pixel_spacing_x 
_em_map.pixel_spacing_y 
_em_map.pixel_spacing_z 
_em_map.size_kb 
_em_map.spacing_x 
_em_map.spacing_y 
_em_map.spacing_z 
_em_map.statistics_average 
_em_map.statistics_maximum 
_em_map.statistics_minimum 
_em_map.statistics_std 
_em_map.symmetry_space_group 
_em_map.type 
EMD-14544 1 'Sharpened map, output from postprocessing.' X Y Z 321.6 90.0 321.6 90.0 321.6 90.0 0.017 author 
'Image stored as floating point number (4 bytes)' 300 300 300 big emd_14544.map.gz              CCP4 
::::EMDATABANK.org::::EMD-14544:::: 299 299 299 0 0 0 1 1.072 1.072 1.072 108001024 300 300 300 3.1954265E-4 0.21614736  
-0.13394156  0.004536797  1 'primary map'    
EMD-14544 2 'Half map from final 3D refinement.'         X Y Z 321.6 90.0 321.6 90.0 321.6 90.0 0.008 author 
'Image stored as floating point number (4 bytes)' 300 300 300 big emd_14544_half_map_1.map.gz   CCP4 
::::EMDATABANK.org::::EMD-14544:::: 299 299 299 0 0 0 1 1.072 1.072 1.072 108001024 300 300 300 1.5652274E-4 0.04513475  
-0.009391842 0.0020310385 1 'half map'       
EMD-14544 3 'Half map from final 3D refinement.'         X Y Z 321.6 90.0 321.6 90.0 321.6 90.0 0.008 author 
'Image stored as floating point number (4 bytes)' 300 300 300 big emd_14544_half_map_2.map.gz   CCP4 
::::EMDATABANK.org::::EMD-14544:::: 299 299 299 0 0 0 2 1.072 1.072 1.072 108001024 300 300 300 1.5619697E-4 0.044961315 
-0.008793963 0.0020307635 1 'half map'       
EMD-14544 4 'Mask used for sharpening.'                  X Y Z 321.6 90.0 321.6 90.0 321.6 90.0 1     author 
'Image stored as floating point number (4 bytes)' 300 300 300 big emd_14544_msk_1.map           CCP4 
::::EMDATABANK.org::::EMD-14544:::: 299 299 299 0 0 0 1 1.072 1.072 1.072 108001024 300 300 300 0.048630092  1.0         0.0 
0.20866296   1 mask             
EMD-14544 5 'Sharpened map, output from LocScale.'       X Y Z 321.6 90.0 321.6 90.0 321.6 90.0 0.1   author 
'Image stored as floating point number (4 bytes)' 300 300 300 big emd_14544_additional_1.map.gz CCP4 
::::EMDATABANK.org::::EMD-14544:::: 299 299 299 0 0 0 1 1.072 1.072 1.072 108001024 300 300 300 0.0023221371 0.50419664  
-0.10149353  0.01745419   1 'additional map' 
EMD-14544 6 'Map from final 3D refinement.'              X Y Z 321.6 90.0 321.6 90.0 321.6 90.0 0.006 author 
'Image stored as floating point number (4 bytes)' 300 300 300 big emd_14544_additional_2.map.gz CCP4 
::::EMDATABANK.org::::EMD-14544:::: 299 299 299 0 0 0 2 1.072 1.072 1.072 108001024 300 300 300 1.5634863E-4 0.043352537 
-0.008487709 0.0019904554 1 'additional map' 
# 
_em_particle_selection.id                       1 
_em_particle_selection.image_processing_id      1 
_em_particle_selection.details                  ? 
_em_particle_selection.method                   ? 
_em_particle_selection.num_particles_selected   909790 
_em_particle_selection.reference_model          ? 
# 
loop_
_em_software.id 
_em_software.category 
_em_software.details 
_em_software.name 
_em_software.version 
_em_software.image_processing_id 
_em_software.fitting_id 
_em_software.imaging_id 
1  'PARTICLE SELECTION'       ? RELION         3.08 1 ? ? 
2  'IMAGE ACQUISITION'        ? EPU            ?    ? ? 1 
3  MASKING                    ? ?              ?    ? ? ? 
4  'CTF CORRECTION'           ? Gctf           ?    1 ? ? 
5  'LAYERLINE INDEXING'       ? ?              ?    ? ? ? 
6  'DIFFRACTION INDEXING'     ? ?              ?    ? ? ? 
7  'MODEL FITTING'            ? 'UCSF Chimera' ?    ? 1 ? 
8  'MODEL FITTING'            ? Coot           ?    ? 1 ? 
9  OTHER                      ? ?              ?    ? ? ? 
10 'MODEL REFINEMENT'         ? REFMAC         ?    ? 1 ? 
11 'INITIAL EULER ASSIGNMENT' ? RELION         3.08 1 ? ? 
12 'FINAL EULER ASSIGNMENT'   ? RELION         3.08 1 ? ? 
13 CLASSIFICATION             ? RELION         3.08 1 ? ? 
14 RECONSTRUCTION             ? RELION         3.08 1 ? ? 
# 
_em_specimen.id                      1 
_em_specimen.experiment_id           1 
_em_specimen.concentration           1 
_em_specimen.details                 ? 
_em_specimen.embedding_applied       NO 
_em_specimen.shadowing_applied       NO 
_em_specimen.staining_applied        NO 
_em_specimen.vitrification_applied   YES 
# 
_em_start_model.id                               1 
_em_start_model.details                          ? 
_em_start_model.image_processing_id              1 
_em_start_model.emdb_id                          EMD-21374 
_em_start_model.insilico_model                   ? 
_em_start_model.orthogonal_tilt_angle1           ? 
_em_start_model.orthogonal_tilt_angle2           ? 
_em_start_model.orthogonal_tilt_num_images       ? 
_em_start_model.other                            ? 
_em_start_model.pdb_id                           ? 
_em_start_model.random_conical_tilt_angle        ? 
_em_start_model.random_conical_tilt_num_images   ? 
_em_start_model.type                             'EMDB MAP' 
# 
_em_support_film.id                  1 
_em_support_film.sample_support_id   1 
_em_support_film.material            CARBON 
_em_support_film.thickness           ? 
_em_support_film.topology            'HOLEY ARRAY' 
# 
loop_
_pdbx_audit_support.funding_organization 
_pdbx_audit_support.country 
_pdbx_audit_support.grant_number 
_pdbx_audit_support.details 
_pdbx_audit_support.ordinal 
'Engineering and Physical Sciences Research Council' 'United Kingdom' P2019-0006    ? 1 
'Wellcome Trust'                                     'United Kingdom' 100209/Z/12/Z ? 2 
# 
_pdbx_initial_refinement_model.id               1 
_pdbx_initial_refinement_model.type             'experimental model' 
_pdbx_initial_refinement_model.source_name      PDB 
_pdbx_initial_refinement_model.accession_code   6ZHD 
# 
