data_EMD-0975
# 
_entry.id   EMD-0975 
# 
_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   6LTN         pdb_00006ltn 10.2210/pdb6ltn/pdb 
WWPDB D_1300015416 ?            ?                   
EMDB  EMD-0975     ?            ?                   
# 
_pdbx_database_related.db_name        EMDB 
_pdbx_database_related.details        'cryo-EM structure of C-terminal truncated human Pannexin1' 
_pdbx_database_related.db_id          EMD-0975 
_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                   CN 
_citation.database_id_Medline       ? 
_citation.details                   ? 
_citation.id                        primary 
_citation.journal_abbrev            'Cell Res.' 
_citation.journal_id_ASTM           ? 
_citation.journal_id_CSD            ? 
_citation.journal_id_ISSN           1001-0602 
_citation.journal_full              ? 
_citation.journal_issue             ? 
_citation.journal_volume            30 
_citation.language                  ? 
_citation.page_first                452 
_citation.page_last                 454 
_citation.title                     'Structural basis for gating mechanism of Pannexin 1 channel.' 
_citation.year                      2020 
_citation.database_id_CSD           ? 
_citation.pdbx_database_id_DOI      10.1038/s41422-020-0313-x 
_citation.pdbx_database_id_PubMed   32284561 
_citation.unpublished_flag          ? 
# 
loop_
_citation_author.citation_id 
_citation_author.name 
_citation_author.ordinal 
_citation_author.identifier_ORCID 
primary 'Mou, L.'  1  ? 
primary 'Ke, M.'   2  ? 
primary 'Song, M.' 3  ? 
primary 'Shan, Y.' 4  ? 
primary 'Xiao, Q.' 5  ? 
primary 'Liu, Q.'  6  ? 
primary 'Li, J.'   7  ? 
primary 'Sun, K.'  8  ? 
primary 'Pu, L.'   9  ? 
primary 'Guo, L.'  10 ? 
primary 'Geng, J.' 11 ? 
primary 'Wu, J.'   12 ? 
primary 'Deng, D.' 13 ? 
# 
_entity.id                         1 
_entity.type                       polymer 
_entity.src_method                 man 
_entity.pdbx_description           Pannexin-1 
_entity.formula_weight             49378.277 
_entity.pdbx_number_of_molecules   7 
_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   
;MAIAQLATEYVFSDFLLKEPTEPKFKGLRLELAVDKMVTCIAVGLPLLLISLAFAQEISIGTQISCFSPSSFSWRQAAFV
DSYCWAAVQQKNSLQSESGNLPLWLHKFFPYILLLFAILLYLPPLFWRFAAAPHICSDLKFIMEELDKVYNRAIKAAKSA
RDLDMRDGACSVPGVTENLGQSLWEVSESHFKYPIVEQYLKTKKNSNNLIIKYISCRLLTLIIILLACIYLGYYFSLSSL
SDEFVCSIKSGILRNDSTVPDQFQCKLIAVGIFQLLSVINLVVYVLLAPVVVYTLFVPFRQKTDVLKVYEILPTFDVLHF
KSEGYNDLSLYNLFLEENISEVKSYKCLKVLENIKSSGQGIDPMLLLTNLGMIKMDVVDGKTPMSAEMREEQGNQTAELQ
GMNIDSETKANNGEKNARQRLLDSSCLEWSHPQFEK
;
# 
_entity_src_gen.entity_id                          1 
_entity_src_gen.pdbx_src_id                        1 
_entity_src_gen.pdbx_alt_source_flag               sample 
_entity_src_gen.pdbx_seq_type                      'Biological sequence' 
_entity_src_gen.pdbx_beg_seq_num                   1 
_entity_src_gen.pdbx_end_seq_num                   436 
_entity_src_gen.gene_src_common_name               Human 
_entity_src_gen.gene_src_genus                     ? 
_entity_src_gen.pdbx_gene_src_gene                 'PANX1, MRS1, UNQ2529/PRO6028' 
_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      'Homo sapiens' 
_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id     9606 
_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      'Insect cell expression vector pTIE1' 
_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id     266783 
_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                   ? 
# 
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 
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-0975 
_exptl.details          ? 
_exptl.method           'ELECTRON MICROSCOPY' 
_exptl.method_details   ? 
# 
_struct_keywords.entry_id        EMD-0975 
_struct_keywords.text            'hemichannel, TRANSPORT PROTEIN' 
_struct_keywords.pdbx_keywords   'TRANSPORT PROTEIN' 
_struct_keywords.pdbx_details    ? 
# 
_struct_ref.id          1 
_struct_ref.db_name     UNP 
_struct_ref.db_code     PANX1_HUMAN 
_struct_ref.entity_id   1 
# 
_em_3d_fitting.entry_id          EMD-0975 
_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-0975 
_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               133330 
_em_3d_reconstruction.resolution                  3.1 
_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            8.0 
_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                 'C-terminal truncated human Pannexin1' 
_em_entity_assembly.source               RECOMBINANT 
_em_entity_assembly.type                 'ORGANELLE OR CELLULAR COMPONENT' 
_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-0975 
_em_imaging.accelerating_voltage            300 
_em_imaging.alignment_procedure             ? 
_em_imaging.c2_aperture_diameter            50 
_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             1500 
_em_imaging.nominal_defocus_min             1000 
_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_vitrification.id                      1 
_em_vitrification.specimen_id             1 
_em_vitrification.chamber_temperature     281 
_em_vitrification.cryogen_name            ETHANE 
_em_vitrification.details                 'blot for 3.5 seconds before plunging' 
_em_vitrification.humidity                100 
_em_vitrification.instrument              'FEI VITROBOT MARK IV' 
_em_vitrification.entry_id                EMD-0975 
_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-0975 
_em_experiment.id                      1 
_em_experiment.aggregation_state       PARTICLE 
_em_experiment.reconstruction_method   'SINGLE PARTICLE' 
_em_experiment.entity_assembly_id      1 
# 
_em_admin.entry_id              EMD-0975 
_em_admin.current_status        REL 
_em_admin.deposition_date       2020-01-23 
_em_admin.deposition_site       PDBJ 
_em_admin.details               ? 
_em_admin.last_update           2024-11-20 
_em_admin.map_release_date      2020-05-13 
_em_admin.obsoleted_date        ? 
_em_admin.title                 'cryo-EM structure of C-terminal truncated human Pannexin1' 
_em_admin.header_release_date   2020-05-13 
# 
loop_
_em_author_list.ordinal 
_em_author_list.author 
1 'Mou, L.Q.' 
2 'Ke, 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    6LTN 
_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               ? 
# 
_em_entity_assembly_recombinant.id                   2 
_em_entity_assembly_recombinant.entity_assembly_id   1 
_em_entity_assembly_recombinant.cell                 ? 
_em_entity_assembly_recombinant.ncbi_tax_id          266783 
_em_entity_assembly_recombinant.organism             'Insect cell expression vector pTIE1' 
_em_entity_assembly_recombinant.plasmid              ? 
_em_entity_assembly_recombinant.strain               ? 
# 
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   ? ? ? 'ANGULAR RECONSTITUTION' 
# 
_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         ? 
_em_image_recording.details                       ? 
_em_image_recording.detector_mode                 ? 
_em_image_recording.film_or_detector_model        'GATAN K3 (6k x 4k)' 
_em_image_recording.num_diffraction_images        ? 
_em_image_recording.num_grids_imaged              ? 
_em_image_recording.num_real_images               ? 
# 
_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    ? 
_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-0975 1 ? X Y Z 217.40001 90.0 217.40001 90.0 217.40001 90.0 0.018 author 'Image stored as floating point number (4 bytes)' 200 
200 200 big emd_0975.map.gz            CCP4 ::::EMDATABANK.org::::EMD-0975:::: 199 199 199 0 0 0 1 1.087 1.087 1.087 32001024 200 
200 200 -0.00027264506 0.13024746 -0.06513346  0.003949442  1 'primary map' 
EMD-0975 2 ? X Y Z 217.40001 90.0 217.40001 90.0 217.40001 90.0 0.014 author 'Image stored as floating point number (4 bytes)' 200 
200 200 big emd_0975_half_map_2.map.gz CCP4 ::::EMDATABANK.org::::EMD-0975:::: 199 199 199 0 0 0 2 1.087 1.087 1.087 32001024 200 
200 200 -0.00027398567 0.06600506 -0.02404034  0.0030326485 1 'half map'    
EMD-0975 3 ? X Y Z 217.40001 90.0 217.40001 90.0 217.40001 90.0 0.014 author 'Image stored as floating point number (4 bytes)' 200 
200 200 big emd_0975_half_map_1.map.gz CCP4 ::::EMDATABANK.org::::EMD-0975:::: 199 199 199 0 0 0 1 1.087 1.087 1.087 32001024 200 
200 200 -2.7130442E-4  0.06699814 -0.024280334 0.0030315435 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 
2  'IMAGE ACQUISITION'        ? ?      ? ? ? 1 
3  MASKING                    ? ?      ? ? ? ? 
4  'CTF CORRECTION'           ? Gctf   ? 1 ? ? 
5  'LAYERLINE INDEXING'       ? ?      ? ? ? ? 
6  'DIFFRACTION INDEXING'     ? ?      ? ? ? ? 
7  'MODEL FITTING'            ? ?      ? ? ? ? 
8  'MODEL REFINEMENT'         ? ?      ? ? ? ? 
9  OTHER                      ? ?      ? ? ? ? 
10 'INITIAL EULER ASSIGNMENT' ? RELION ? 1 ? ? 
11 'FINAL EULER ASSIGNMENT'   ? ?      ? 1 ? ? 
12 CLASSIFICATION             ? ?      ? 1 ? ? 
13 RECONSTRUCTION             ? ?      ? 1 ? ? 
# 
_em_specimen.id                      1 
_em_specimen.experiment_id           1 
_em_specimen.concentration           5.0 
_em_specimen.details                 'This sample was monodisperse' 
_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 
# 
