data_EMD-14174
# 
_entry.id   EMD-14174 
# 
_audit_conform.dict_name       mmcif_pdbx.dic 
_audit_conform.dict_version    5.399 
_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   7QVC         pdb_00007qvc 10.2210/pdb7qvc/pdb 
WWPDB D_1292120387 ?            ?                   
EMDB  EMD-14174    ?            ?                   
# 
_pdbx_database_related.db_name        EMDB 
_pdbx_database_related.details        
;TMEM106B filaments with Fold I from Alzheimer's disease (case 1)
;
_pdbx_database_related.db_id          EMD-14174 
_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                   UK 
_citation.database_id_Medline       ? 
_citation.details                   ? 
_citation.id                        primary 
_citation.journal_abbrev            Nature 
_citation.journal_id_ASTM           NATUAS 
_citation.journal_id_CSD            0006 
_citation.journal_id_ISSN           1476-4687 
_citation.journal_full              ? 
_citation.journal_issue             ? 
_citation.journal_volume            605 
_citation.language                  ? 
_citation.page_first                310 
_citation.page_last                 314 
_citation.title                     'Age-dependent formation of TMEM106B amyloid filaments in human brains.' 
_citation.year                      2022 
_citation.database_id_CSD           ? 
_citation.pdbx_database_id_DOI      10.1038/s41586-022-04650-z 
_citation.pdbx_database_id_PubMed   35344985 
_citation.pdbx_database_id_patent   ? 
_citation.unpublished_flag          ? 
# 
loop_
_citation_author.citation_id 
_citation_author.name 
_citation_author.ordinal 
_citation_author.identifier_ORCID 
primary 'Schweighauser, M.'   1  ? 
primary 'Arseni, D.'          2  ? 
primary 'Bacioglu, M.'        3  ? 
primary 'Huang, M.'           4  ? 
primary 'Lovestam, S.'        5  ? 
primary 'Shi, Y.'             6  ? 
primary 'Yang, Y.'            7  ? 
primary 'Zhang, W.'           8  ? 
primary 'Kotecha, A.'         9  ? 
primary 'Garringer, H.J.'     10 ? 
primary 'Vidal, R.'           11 ? 
primary 'Hallinan, G.I.'      12 ? 
primary 'Newell, K.L.'        13 ? 
primary 'Tarutani, A.'        14 ? 
primary 'Murayama, S.'        15 ? 
primary 'Miyazaki, M.'        16 ? 
primary 'Saito, Y.'           17 ? 
primary 'Yoshida, M.'         18 ? 
primary 'Hasegawa, K.'        19 ? 
primary 'Lashley, T.'         20 ? 
primary 'Revesz, T.'          21 ? 
primary 'Kovacs, G.G.'        22 ? 
primary 'van Swieten, J.'     23 ? 
primary 'Takao, M.'           24 ? 
primary 'Hasegawa, M.'        25 ? 
primary 'Ghetti, B.'          26 ? 
primary 'Spillantini, M.G.'   27 ? 
primary 'Ryskeldi-Falcon, B.' 28 ? 
primary 'Murzin, A.G.'        29 ? 
primary 'Goedert, M.'         30 ? 
primary 'Scheres, S.H.W.'     31 ? 
# 
_entity.id                         1 
_entity.type                       polymer 
_entity.src_method                 nat 
_entity.pdbx_description           'Transmembrane protein 106B' 
_entity.formula_weight             31142.295 
_entity.pdbx_number_of_molecules   3 
_entity.pdbx_ec                    ? 
_entity.pdbx_mutation              ? 
_entity.pdbx_fragment              ? 
_entity.details                    ? 
# 
_entity_poly.entity_id                  1 
_entity_poly.type                       'polypeptide(L)' 
_entity_poly.pdbx_seq_one_letter_code   
;MGKSLSHLPLHSSKEDAYDGVTSENMRNGLVNSEVHNEDGRNGDVSQFPYVEFTGRDSVTCPTCQGTGRIPRGQENQLVA
LIPYSDQRLRPRRTKLYVMASVFVCLLLSGLAVFFLFPRSIDVKYIGVKSAYVSYDVQKRTIYLNITNTLNITNNNYYSV
EVENITAQVQFSKTVIGKARLNNISIIGPLDMKQIDYTVPTVIAEEMSYMYDFCTLISIKVHNIVLMMQVTVTTTYFGHS
EQISQERYQYVDCGRNTTYQLGQSEYLNVLQPQQ
;
# 
_entity_src_nat.entity_id                  1 
_entity_src_nat.pdbx_src_id                1 
_entity_src_nat.pdbx_alt_source_flag       sample 
_entity_src_nat.pdbx_beg_seq_num           1 
_entity_src_nat.pdbx_end_seq_num           274 
_entity_src_nat.common_name                human 
_entity_src_nat.pdbx_organism_scientific   'Homo sapiens' 
_entity_src_nat.pdbx_ncbi_taxonomy_id      9606 
_entity_src_nat.genus                      ? 
_entity_src_nat.species                    ? 
_entity_src_nat.strain                     ? 
_entity_src_nat.tissue                     ? 
_entity_src_nat.tissue_fraction            ? 
_entity_src_nat.pdbx_secretion             ? 
_entity_src_nat.pdbx_fragment              ? 
_entity_src_nat.pdbx_variant               ? 
_entity_src_nat.pdbx_cell_line             ? 
_entity_src_nat.pdbx_atcc                  ? 
_entity_src_nat.pdbx_culture_collection    ? 
_entity_src_nat.pdbx_cellular_location     ? 
_entity_src_nat.pdbx_organ                 ? 
_entity_src_nat.pdbx_organelle             ? 
_entity_src_nat.pdbx_cell                  ? 
_entity_src_nat.pdbx_plasmid_name          ? 
_entity_src_nat.pdbx_plasmid_details       ? 
_entity_src_nat.details                    ? 
# 
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 
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 
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-14174 
_exptl.details          ? 
_exptl.method           'ELECTRON MICROSCOPY' 
_exptl.method_details   ? 
# 
_struct_keywords.entry_id        EMD-14174 
_struct_keywords.text            'Amyloid, neurodegeneration, filament, TMEM106B, PROTEIN FIBRIL' 
_struct_keywords.pdbx_keywords   'PROTEIN FIBRIL' 
_struct_keywords.pdbx_details    ? 
# 
_struct_ref.id          1 
_struct_ref.db_name     UNP 
_struct_ref.db_code     T106B_HUMAN 
_struct_ref.entity_id   1 
# 
_em_3d_fitting.entry_id          EMD-14174 
_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         ? 
_em_3d_fitting.target_criteria   ? 
_em_3d_fitting.method            ? 
# 
_em_3d_reconstruction.entry_id                    EMD-14174 
_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               47414 
_em_3d_reconstruction.resolution                  2.64 
_em_3d_reconstruction.resolution_method           'FSC 0.143 CUT-OFF' 
_em_3d_reconstruction.symmetry_type               HELICAL 
_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            7.4 
_em_buffer.specimen_id   1 
_em_buffer.name          ? 
# 
_em_entity_assembly.id                   1 
_em_entity_assembly.parent_id            0 
_em_entity_assembly.details              ? 
_em_entity_assembly.go_id                ? 
_em_entity_assembly.name                 TMEM106B 
_em_entity_assembly.source               NATURAL 
_em_entity_assembly.type                 TISSUE 
_em_entity_assembly.chimera              NO 
_em_entity_assembly.entity_id_list       1 
_em_entity_assembly.ipr_id               ? 
_em_entity_assembly.synonym              ? 
_em_entity_assembly.number_of_copies     ? 
_em_entity_assembly.oligomeric_details   ? 
# 
_em_imaging.id                              1 
_em_imaging.entry_id                        EMD-14174 
_em_imaging.accelerating_voltage            300 
_em_imaging.alignment_procedure             ? 
_em_imaging.c2_aperture_diameter            ? 
_em_imaging.calibrated_defocus_max          ? 
_em_imaging.calibrated_defocus_min          ? 
_em_imaging.calibrated_magnification        ? 
_em_imaging.cryogen                         ? 
_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                      ? 
_em_imaging.nominal_defocus_max             3000 
_em_imaging.nominal_defocus_min             1200 
_em_imaging.nominal_magnification           ? 
_em_imaging.recording_temperature_maximum   ? 
_em_imaging.recording_temperature_minimum   ? 
_em_imaging.residual_tilt                   ? 
_em_imaging.specimen_holder_model           ? 
_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_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              ? 
_em_vitrification.entry_id                EMD-14174 
_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-14174 
_em_experiment.id                      1 
_em_experiment.aggregation_state       FILAMENT 
_em_experiment.reconstruction_method   HELICAL 
_em_experiment.entity_assembly_id      1 
# 
_em_admin.entry_id              EMD-14174 
_em_admin.current_status        REL 
_em_admin.deposition_date       2022-01-21 
_em_admin.deposition_site       PDBE 
_em_admin.details               ? 
_em_admin.last_update           2024-11-20 
_em_admin.map_release_date      2022-03-09 
_em_admin.obsoleted_date        ? 
_em_admin.title                 
;TMEM106B filaments with Fold I from Alzheimer's disease (case 1)
;
_em_admin.header_release_date   2022-03-09 
# 
loop_
_em_author_list.ordinal 
_em_author_list.author 
_em_author_list.identifier_ORCID 
1 'Lovestam, S.'      ? 
2 'Schweighauser, M.' ? 
# 
_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    7QVC 
_em_db_reference.db_name        PDB 
_em_db_reference.details        ? 
_em_db_reference.relationship   'IN FRAME' 
# 
_em_entity_assembly_naturalsource.id                   2 
_em_entity_assembly_naturalsource.entity_assembly_id   1 
_em_entity_assembly_naturalsource.cell                 ? 
_em_entity_assembly_naturalsource.cellular_location    ? 
_em_entity_assembly_naturalsource.ncbi_tax_id          9606 
_em_entity_assembly_naturalsource.organ                ? 
_em_entity_assembly_naturalsource.organelle            ? 
_em_entity_assembly_naturalsource.organism             'Homo sapiens' 
_em_entity_assembly_naturalsource.strain               ? 
_em_entity_assembly_naturalsource.tissue               ? 
# 
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 ? ? ? 'NOT APPLICABLE' 
2 ? 1 FINAL   ? ? ? 'NOT APPLICABLE' 
# 
_em_helical_entity.id                             1 
_em_helical_entity.image_processing_id            1 
_em_helical_entity.angular_rotation_per_subunit   -0.42 
_em_helical_entity.axial_rise_per_subunit         4.81 
_em_helical_entity.axial_symmetry                 C1 
_em_helical_entity.details                        ? 
_em_helical_entity.entity_assembly_id             1 
# 
_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         40 
_em_image_recording.average_exposure_time               ? 
_em_image_recording.details                             ? 
_em_image_recording.detector_mode                       ? 
_em_image_recording.film_or_detector_model              'FEI FALCON IV (4k x 4k)' 
_em_image_recording.num_diffraction_images              ? 
_em_image_recording.num_grids_imaged                    ? 
_em_image_recording.num_real_images                     ? 
_em_image_recording.avg_electron_dose_per_subtomogram   ? 
# 
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-14174 1 
;Sharpened map of TMEM106B filaments with Fold I from Alzheimer's disease (case 1)
;
X Y Z 232.64 90.0 232.64 90.0 232.64 90.0 0.0068  author 'Image stored as floating point number (4 bytes)' 320 320 320 big 
emd_14174.map.gz            CCP4 ::::EMDATABANK.org::::EMD-14174:::: 319 319 319 0 0 0 1 0.727 0.727 0.727 131073024 320 320 320 
1.2165702E-4 0.025287697 -0.011593033 0.001470615  1 'primary map' 
EMD-14174 2 
;Half map 1 of TMEM106B filaments with Fold I from Alzheimer's disease (case 1)
;
X Y Z 232.64 90.0 232.64 90.0 232.64 90.0 0.00668 author 'Image stored as floating point number (4 bytes)' 320 320 320 big 
emd_14174_half_map_2.map.gz CCP4 ::::EMDATABANK.org::::EMD-14174:::: 319 319 319 0 0 0 2 0.727 0.727 0.727 131073024 320 320 320 
6.2792795E-5 0.025858825 -0.016394677 0.0020570792 1 'half map'    
EMD-14174 3 
;Half map 2 of TMEM106B filaments with Fold I from Alzheimer's disease (case 1)
;
X Y Z 232.64 90.0 232.64 90.0 232.64 90.0 0.00668 author 'Image stored as floating point number (4 bytes)' 320 320 320 big 
emd_14174_half_map_1.map.gz CCP4 ::::EMDATABANK.org::::EMD-14174:::: 319 319 319 0 0 0 1 0.727 0.727 0.727 131073024 320 320 320 
6.869359E-5  0.02654793  -0.017026497 0.0020475409 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  'CRYSTALLOGRAPHY MERGING'  ?                                      ?      ?   1 1 1 
2  'IMAGE ACQUISITION'        
;It's a good programme, thanks Sjors!
;
RELION 4.0 ? ? 1 
3  MASKING                    ?                                      ?      ?   ? ? ? 
4  'CTF CORRECTION'           ?                                      ?      ?   1 ? ? 
5  'LAYERLINE INDEXING'       ?                                      ?      ?   ? ? ? 
6  'DIFFRACTION INDEXING'     ?                                      ?      ?   ? ? ? 
7  'MODEL FITTING'            ?                                      ?      ?   ? ? ? 
8  'MODEL REFINEMENT'         ?                                      ?      ?   ? ? ? 
9  OTHER                      ?                                      ?      ?   ? ? ? 
10 'INITIAL EULER ASSIGNMENT' ?                                      ?      ?   1 ? ? 
11 'FINAL EULER ASSIGNMENT'   ?                                      ?      ?   1 ? ? 
12 CLASSIFICATION             ?                                      ?      ?   1 ? ? 
13 RECONSTRUCTION             'Good stuff.'                          RELION 4.0 1 ? ? 
# 
_em_specimen.id                      1 
_em_specimen.experiment_id           1 
_em_specimen.concentration           ? 
_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                          ? 
_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                             NONE 
# 
_pdbx_audit_support.funding_organization   'Medical Research Council (MRC, United Kingdom)' 
_pdbx_audit_support.country                'United Kingdom' 
_pdbx_audit_support.grant_number           ? 
_pdbx_audit_support.details                ? 
_pdbx_audit_support.ordinal                1 
# 
