data_EMD-0433
# 
_entry.id   EMD-0433 
# 
_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   6NC2         pdb_00006nc2 10.2210/pdb6nc2/pdb 
WWPDB D_1000238525 ?            ?                   
EMDB  EMD-0433     ?            ?                   
# 
_pdbx_database_related.db_name        EMDB 
_pdbx_database_related.details        
'AMC011 v4.2 SOSIP Env trimer in complex with fusion peptide targeting antibody ACS202 fragment antigen binding' 
_pdbx_database_related.db_id          EMD-0433 
_pdbx_database_related.content_type   '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            'Cell Host Microbe' 
_citation.journal_id_ASTM           ? 
_citation.journal_id_CSD            ? 
_citation.journal_id_ISSN           1934-6069 
_citation.journal_full              ? 
_citation.journal_issue             ? 
_citation.journal_volume            25 
_citation.language                  ? 
_citation.page_first                873 
_citation.page_last                 ? 
_citation.title                     
'Conformational Plasticity in the HIV-1 Fusion Peptide Facilitates Recognition by Broadly Neutralizing Antibodies.' 
_citation.year                      2019 
_citation.database_id_CSD           ? 
_citation.pdbx_database_id_DOI      10.1016/j.chom.2019.04.011 
_citation.pdbx_database_id_PubMed   31194940 
_citation.unpublished_flag          ? 
# 
loop_
_citation_author.citation_id 
_citation_author.name 
_citation_author.ordinal 
_citation_author.identifier_ORCID 
primary 'Yuan, M.'       1  ? 
primary 'Cottrell, C.A.' 2  ? 
primary 'Ozorowski, G.'  3  ? 
primary 'van Gils, M.J.' 4  ? 
primary 'Kumar, S.'      5  ? 
primary 'Wu, N.C.'       6  ? 
primary 'Sarkar, A.'     7  ? 
primary 'Torres, J.L.'   8  ? 
primary 'de Val, N.'     9  ? 
primary 'Copps, J.'      10 ? 
primary 'Moore, J.P.'    11 ? 
primary 'Sanders, R.W.'  12 ? 
primary 'Ward, A.B.'     13 ? 
primary 'Wilson, I.A.'   14 ? 
# 
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 'AMC011 v4.2 SOSIP gp120' 57668.938 6  ? 'H66R, A316W, A501C'         ? ? 
2 polymer     man 'AMC011 v4.2 SOSIP gp41' 17300.666 6  ? 'L543Q, I559P, Q567K, T605C' ? ? 
3 polymer     man 'Monoclonal antibody ACS202 fragment antigen binding heavy chain' 27392.023 6  ? ?                            ? 
? 
4 polymer     man 'Monoclonal antibody ACS202 fragment antigen binding kappa chain' 25475.658 6  ? ?                            ? 
? 
5 branched    man 
;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
;
910.823   12 ? ?                            ? ? 
6 branched    man '2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose' 424.401   6  ? ? ? ? 
7 branched    man 
;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
;
1072.964  6  ? ?                            ? ? 
8 non-polymer man 2-acetamido-2-deoxy-beta-D-glucopyranose 221.208   30 ? ?                            ? ? 
# 
loop_
_entity_poly.entity_id 
_entity_poly.type 
_entity_poly.pdbx_seq_one_letter_code 
1 'polypeptide(L)' 
;MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARAEQLWVTVYYGVPVWKEATTTLFCASDARAYDTEVRNVWATHACV
PTDPNPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTDLRNATNTNATNTTSSSRGTMEG
GEIKNCSFNITTSMRDKVQKEYALFYKLDVVPIKNDNTSYRLISCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNDK
KFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSANFTDNAKIIIVQLNKSVEINCTRPNNNTRKSIHIGP
GRWFYTTGEIIGDIRQAHCNISGTKWNDTLKQIVVKLKEQFGNKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNS
TWNDGSNYTGTIVLPCRIKQIVNMWQEVGKAMYAPPIKGQIRCSSNITGLILIRDGGKNRSENTEIFRPGGGDMRDNWRS
ELYKYKVVKIEPLGIAPTKCKRRVVQRRRRRR
;
2 'polypeptide(L)' 
;AVGIGAVFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQNNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLKDQQ
LLGIWGCSGKLICCTAVPWNTSWSNKSYNQIWNNMTWMEWEREIDNYTSLIYTLIEDSQNQQEKNEQELLELD
;
3 'polypeptide(L)' 
;MELGLRWVFLVAILEVHSQVQLVESGGGVVQPGGSLRLSCAASGFAFKDFGMHWVRQAPGKGLEWVAVIGGGHGQHQSYS
ESVKGRFAITRDNEKNKLYLHMDRLRTEDTAVYYCAKDRLGRPWNIGGRLVYYYYGMDVWGQGTTVTVSSASTKGPSVFP
LAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPS
NTKVDKKVEPKSCD
;
4 'polypeptide(L)' 
;MGWSCIILFLVATATGVHCAIRMTQSPSSLSASVGDRVTITCQASQDIKKSLNWYRQKPGKAPELLIHDASILQTGVPSA
FTASGSGTHFSFVINKLQPEDVGTYFCQEYENLQFTFGPGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYP
REAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
;
# 
_pdbx_entity_nonpoly.entity_id   8 
_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' 1 512 ?     ? ? ? ? ? ? ? ? 'Human immunodeficiency virus 1' 11676 ? ? ? ? ? ? ? ? human 
'Homo sapiens' 9606 ? ? ? ? ? ? ? ? HEK293F ? ? ? ? ? ? ? ? ? ? ? ? 
2 1 sample 'Biological sequence' 1 153 ?     ? ? ? ? ? ? ? ? 'Human immunodeficiency virus 1' 11676 ? ? ? ? ? ? ? ? human 
'Homo sapiens' 9606 ? ? ? ? ? ? ? ? HEK293F ? ? ? ? ? ? ? ? ? ? ? ? 
3 1 sample 'Biological sequence' 1 254 human ? ? ? ? ? ? ? ? 'Homo sapiens'                   9606  ? ? ? ? ? ? ? ? human 
'Homo sapiens' 9606 ? ? ? ? ? ? ? ? HEK293F ? ? ? ? ? ? ? ? ? ? ? ? 
4 1 sample 'Biological sequence' 1 233 human ? ? ? ? ? ? ? ? 'Homo sapiens'                   9606  ? ? ? ? ? ? ? ? human 
'Homo sapiens' 9606 ? ? ? ? ? ? ? ? HEK293F ? ? ? ? ? ? ? ? ? ? ? ? 
# 
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 
BMA 'D-saccharide, beta linking'  . beta-D-mannopyranose                     'beta-D-mannose; D-mannose; mannose' 'C6 H12 O6'      
180.156 
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 
MAN 'D-saccharide, alpha linking' . alpha-D-mannopyranose                    'alpha-D-mannose; D-mannose; mannose' 'C6 H12 O6' 
180.156 
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-0433 
_exptl.details          ? 
_exptl.method           'ELECTRON MICROSCOPY' 
_exptl.method_details   ? 
# 
_struct_keywords.entry_id        EMD-0433 
_struct_keywords.text            
'HIV-1 Env, SOSIP, trimer, broadly neutralizing antibody, fusion peptide, VIRAL PROTEIN, IMMUNE SYSTEM' 
_struct_keywords.pdbx_keywords   'IMMUNE SYSTEM' 
_struct_keywords.pdbx_details    ? 
# 
loop_
_struct_ref.id 
_struct_ref.db_name 
_struct_ref.db_code 
_struct_ref.entity_id 
1 PDB 6NC2 1 
2 PDB 6NC2 2 
3 PDB 6NC2 3 
4 PDB 6NC2 4 
# 
_em_3d_fitting.entry_id          EMD-0433 
_em_3d_fitting.id                1 
_em_3d_fitting.details           ? 
_em_3d_fitting.overall_b_value   ? 
_em_3d_fitting.ref_protocol      ? 
_em_3d_fitting.ref_space         REAL 
_em_3d_fitting.target_criteria   ? 
_em_3d_fitting.method            ? 
# 
_em_3d_reconstruction.entry_id                    EMD-0433 
_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          ? 
_em_3d_reconstruction.num_particles               49878 
_em_3d_reconstruction.resolution                  5.20 
_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_3d_reconstruction.citation_id                 ? 
_em_3d_reconstruction.euler_angles_details        ? 
# 
_em_buffer.id            1 
_em_buffer.details       'Detergent (DDM) added immediately prior to grid preparation' 
_em_buffer.pH            7.4 
_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.entity_id_list 
_em_entity_assembly.ipr_id 
_em_entity_assembly.synonym 
_em_entity_assembly.number_of_copies 
_em_entity_assembly.oligomeric_details 
_em_entity_assembly.mutant_flag 
1 0 ? ? 'Complex of AMC011 v4.2 SOSIP trimer and ACS202 fragment antigen binding' 'MULTIPLE SOURCES' COMPLEX 1,2,3,4 ? ? ? ? ? 
2 1 ? ? 'HIV-1 Env AMC011 v4.2 SOSIP gp120'                                       RECOMBINANT        COMPLEX 1       ? ? ? ? ? 
3 1 ? ? 'HIV-1 Env AMC011 v4.2 SOSIP gp41'                                        RECOMBINANT        COMPLEX 2       ? ? ? ? ? 
4 1 ? ? VRC34.01                                                                  RECOMBINANT        COMPLEX 3,4     ? ? ? ? ? 
# 
_em_image_scans.entry_id                EMD-0433 
_em_image_scans.id                      1 
_em_image_scans.dimension_height        3838 
_em_image_scans.dimension_width         3710 
_em_image_scans.frames_per_image        50 
_em_image_scans.image_recording_id      1 
_em_image_scans.sampling_size           5 
_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-0433 
_em_imaging.accelerating_voltage            300 
_em_imaging.alignment_procedure             'COMA FREE' 
_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                         ? 
_em_imaging.electron_source                 'FIELD EMISSION GUN' 
_em_imaging.illumination_mode               'FLOOD BEAM' 
_em_imaging.microscope_model                'FEI TITAN KRIOS' 
_em_imaging.mode                            'BRIGHT FIELD' 
_em_imaging.nominal_cs                      2.7 
_em_imaging.nominal_defocus_max             2500 
_em_imaging.nominal_defocus_min             1300 
_em_imaging.nominal_magnification           29000 
_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_imaging.microscope_id                   ? 
# 
_em_sample_support.id               1 
_em_sample_support.specimen_id      1 
_em_sample_support.details          'Gatan Solarus 950 Plasma system' 
_em_sample_support.grid_material    COPPER 
_em_sample_support.grid_mesh_size   400 
_em_sample_support.grid_type        'C-flat-2/2 4C' 
_em_sample_support.method           ? 
_em_sample_support.film_material    ? 
_em_sample_support.pretreatment     ? 
_em_sample_support.citation_id      ? 
# 
_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              'HOMEMADE PLUNGER' 
_em_vitrification.entry_id                EMD-0433 
_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-0433 
_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-0433 
_em_single_particle_entity.id                    1 
_em_single_particle_entity.image_processing_id   1 
_em_single_particle_entity.point_symmetry        D3 
# 
_em_admin.entry_id              EMD-0433 
_em_admin.current_status        REL 
_em_admin.deposition_date       2018-12-10 
_em_admin.deposition_site       RCSB 
_em_admin.details               ? 
_em_admin.last_update           2024-11-06 
_em_admin.map_release_date      2019-06-19 
_em_admin.obsoleted_date        ? 
_em_admin.title                 
'AMC011 v4.2 SOSIP Env trimer in complex with fusion peptide targeting antibody ACS202 fragment antigen binding' 
_em_admin.header_release_date   2019-01-16 
# 
loop_
_em_author_list.ordinal 
_em_author_list.author 
1 'Ozorowski, G.'  
2 'de Val, N.'     
3 'Cottrell, C.A.' 
4 'Copps, J.'      
5 'Ward, A.B.'     
# 
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 50   mM ?    Tris                         
1 2 150  mM NaCl 'Sodium chloride'            
1 3 0.06 mM ?    'n-dodecyl beta-D-maltoside' 
# 
_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    6NC2 
_em_db_reference.db_name        PDB 
_em_db_reference.details        ? 
_em_db_reference.relationship   'IN FRAME' 
# 
_em_entity_assembly_molwt.entity_assembly_id   1 
_em_entity_assembly_molwt.id                   1 
_em_entity_assembly_molwt.experimental_flag    NO 
_em_entity_assembly_molwt.units                MEGADALTONS 
_em_entity_assembly_molwt.value                0.57 
# 
loop_
_em_entity_assembly_naturalsource.cellular_location 
_em_entity_assembly_naturalsource.entity_assembly_id 
_em_entity_assembly_naturalsource.id 
_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 
_em_entity_assembly_naturalsource.cell 
? 2 1 11676 ? ? 'Human immunodeficiency virus 1' ? ? ? 
? 3 2 11676 ? ? 'Human immunodeficiency virus 1' ? ? ? 
? 4 3 9606  ? ? 'Homo sapiens'                   ? ? ? 
# 
loop_
_em_entity_assembly_recombinant.entity_assembly_id 
_em_entity_assembly_recombinant.id 
_em_entity_assembly_recombinant.ncbi_tax_id 
_em_entity_assembly_recombinant.organism 
_em_entity_assembly_recombinant.plasmid 
_em_entity_assembly_recombinant.strain 
_em_entity_assembly_recombinant.cell 
2 1 9606 'Homo sapiens' ? ? ? 
3 2 9606 'Homo sapiens' ? ? ? 
4 3 9606 'Homo sapiens' ? ? ? 
# 
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 ? ? ? 'PROJECTION MATCHING' 
2 ? 1 FINAL   ? ? ? 'PROJECTION MATCHING' 
# 
_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                ? 
# 
_em_grid_pretreatment.id                  1 
_em_grid_pretreatment.sample_support_id   1 
_em_grid_pretreatment.atmosphere          Ar/O2 
_em_grid_pretreatment.pressure            ? 
_em_grid_pretreatment.time                10 
_em_grid_pretreatment.type                'PLASMA CLEANING' 
# 
_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   92 
_em_image_recording.average_exposure_time         10 
_em_image_recording.details                       ? 
_em_image_recording.detector_mode                 COUNTING 
_em_image_recording.film_or_detector_model        'GATAN K2 SUMMIT (4k x 4k)' 
_em_image_recording.num_diffraction_images        ? 
_em_image_recording.num_grids_imaged              ? 
_em_image_recording.num_real_images               1641 
# 
_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          ? 
_em_imaging_optics.energyfilter_upper         ? 
_em_imaging_optics.energyfilter_slit_width    ? 
_em_imaging_optics.phase_plate                ? 
_em_imaging_optics.sph_aberration_corrector   ? 
# 
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-0433 1 'sharpened map'                 X Y Z 296.63998 90.0 296.63998 90.0 296.63998 90.0 0.04  author 
'Image stored as floating point number (4 bytes)' 288 288 288 big emd_0433.map.gz            CCP4 
::::EMDATABANK.org::::EMD-0433:::: 287 287 287 0 0 0 1 1.03 1.03 1.03 95552512 288 288 288 0.0015213995 0.09938333  -0.030829472 
0.008293105  1 'primary map' 
EMD-0433 2 'mask used for post-processing' X Y Z 296.63998 90.0 296.63998 90.0 296.63998 90.0 0.5   author 
'Image stored as floating point number (4 bytes)' 288 288 288 big emd_0433_msk_1.map         CCP4 
::::EMDATABANK.org::::EMD-0433:::: 287 287 287 0 0 0 1 1.03 1.03 1.03 95552512 288 288 288 0.10499145   1.0         0.0          
0.2917533    1 mask          
EMD-0433 3 'Half map 1'                    X Y Z 296.63998 90.0 296.63998 90.0 296.63998 90.0 0.015 author 
'Image stored as floating point number (4 bytes)' 288 288 288 big emd_0433_half_map_2.map.gz CCP4 
::::EMDATABANK.org::::EMD-0433:::: 287 287 287 0 0 0 2 1.03 1.03 1.03 95552512 288 288 288 7.6647586E-4 0.02595192  -0.005369458 
0.0033768204 1 'half map'    
EMD-0433 4 'Half map 2'                    X Y Z 296.63998 90.0 296.63998 90.0 296.63998 90.0 0.015 author 
'Image stored as floating point number (4 bytes)' 288 288 288 big emd_0433_half_map_1.map.gz CCP4 
::::EMDATABANK.org::::EMD-0433:::: 287 287 287 0 0 0 1 1.03 1.03 1.03 95552512 288 288 288 7.549236E-4  0.024912762 -0.005094552 
0.0033606938 1 'half map'    
# 
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'       ? 'DoG Picker' ?    1 ? ? 
2  'IMAGE ACQUISITION'        ? Leginon      ?    ? ? 1 
3  MASKING                    ? ?            ?    ? ? ? 
4  'CTF CORRECTION'           ? Gctf         1.06 1 ? ? 
5  'LAYERLINE INDEXING'       ? ?            ?    ? ? ? 
6  'DIFFRACTION INDEXING'     ? ?            ?    ? ? ? 
7  'MODEL FITTING'            ? ?            ?    ? 1 ? 
8  OTHER                      ? ?            ?    ? ? ? 
9  'INITIAL EULER ASSIGNMENT' ? RELION       2.1  1 ? ? 
10 'FINAL EULER ASSIGNMENT'   ? RELION       2.1  1 ? ? 
11 CLASSIFICATION             ? RELION       2.1  1 ? ? 
12 RECONSTRUCTION             ? RELION       2.1  1 ? ? 
13 'MODEL REFINEMENT'         ? Rosetta      3.10 ? 1 ? 
# 
_em_specimen.id                      1 
_em_specimen.experiment_id           1 
_em_specimen.concentration           5 
_em_specimen.details                 'SEC purified sample after overnight incubation of molar excess Fab to trimer' 
_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                          'PDB coordinates converted to low pass filtered map' 
_em_start_model.image_processing_id              1 
_em_start_model.emdb_id                          ? 
_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                           4ZMJ 
_em_start_model.random_conical_tilt_angle        ? 
_em_start_model.random_conical_tilt_num_images   ? 
_em_start_model.type                             'PDB ENTRY' 
# 
_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 
# 
_em_tomography_specimen.id                       1 
_em_tomography_specimen.specimen_id              1 
_em_tomography_specimen.cryo_protectant          ? 
_em_tomography_specimen.details                  ? 
_em_tomography_specimen.fiducial_markers         ? 
_em_tomography_specimen.high_pressure_freezing   ? 
_em_tomography_specimen.sectioning               ? 
# 
loop_
_pdbx_audit_support.funding_organization 
_pdbx_audit_support.country 
_pdbx_audit_support.grant_number 
_pdbx_audit_support.details 
_pdbx_audit_support.ordinal 
'National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)' 'United States' 'P01 AI110657' ? 
1 
'Bill & Melinda Gates Foundation'                                                                 'United States' OPP1115782     ? 
2 
'Bill & Melinda Gates Foundation'                                                                 'United States' OPP1084519     ? 
3 
'National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)' 'United States' 'F31 Al131873' ? 
4 
'Other private'                                                                                   'United States' 109718-63-RKNT ? 
5 
# 
