2025-06-04 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name DATABASE_REFERENCES citation _citation.journal_volume _citation.page_first _citation.page_last EXPERIMENTAL_PREPARATION em_sample_support _em_sample_support.grid_type AUTHOR_SUPPORTING_EVIDENCE pdbx_audit_support _pdbx_audit_support.funding_organization REMEDIATION REPOSITORY Carbohydrate remediation STRUCTURE_SUMMARY atom_site chem_comp entity pdbx_branch_scheme pdbx_chem_comp_identifier pdbx_entity_branch pdbx_entity_branch_descriptor pdbx_entity_branch_link pdbx_entity_branch_list pdbx_entity_nonpoly pdbx_nonpoly_scheme pdbx_struct_assembly_gen pdbx_unobs_or_zero_occ_atoms pdbx_validate_close_contact struct_asym struct_conn struct_site struct_site_gen _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.label_asym_id _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_entity_id _atom_site.type_symbol _chem_comp.name _chem_comp.type _entity.formula_weight _entity.pdbx_description _entity.pdbx_number_of_molecules _entity.type _pdbx_struct_assembly_gen.asym_id_list _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.auth_seq_id_2 _struct_conn.pdbx_role _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id STRUCTURE_SUMMARY chem_comp chem_comp_atom chem_comp_bond database_2 em_admin pdbx_entry_details pdbx_modification_feature _chem_comp.pdbx_synonyms _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_admin.last_update DATA_COLLECTION em_admin em_software _em_admin.last_update _em_software.name RCSB RCSB 2017-03-20 2017-05-10 2017-08-16 2025-06-04 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01GM052586 United States Cryo-EM structure of ERAD-associated E3 ubiquitin-protein ligase component HRD3 Mi W Schoebel S Hrd3 ERAD, PROTEIN TRANSPORT Schoebel S Mi W Stein A Ovchinnikov S Pavlovicz R DiMaio F Baker D Chambers MG Su H Li D Rapoport TA Liao M Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3. Nature UK 548 352 355 2017 28682307 doi:10.1038/nature23314 1476-4687 0006 NATUAS EMD-8637 other EM volume
CryoEM structure of the ERAD-associated E3 ubiquitin-protein ligase HRD1
 EMD-8638 other EM volume
Cryo-EM map of the ERAD components Hrd1/Hrd3 dimer
 EMD-8639 other EM volume
CryoEM map of Hrd1 dimer with one Hrd3 molecule
 5v7v FULLOVERLAP Hrd1/Hrd3 complex Hrd1/Hrd3 complex 0 1 Saccharomyces cerevisiae S288c ERAD-associated E3 ubiquitin-protein ligase component HRD3 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.093759156 1 Saccharomyces cerevisiae LEVO MITLLLYLCVICNAIVLIRADSIADPWPEARHLLNTIAKSRDPMKEAAMEPNADEFVGFYVPMDYSPRNEEKNYQSIWQN EITDSQRHIYELLVQSSEQFNNSEATYTLSQIHLWSQYNFPHNMTLAHKYLEKFNDLTHFTNHSAIFDLAVMYATGGCAS GNDQTVIPQDSAKALLYYQRAAQLGNLKAKQVLAYKYYSGFNVPRNFHKSLVLYRDIAEQLRKSYSRDEWDIVFPYWESY NVRISDFESGLLGKGLNSVPSSTVRKRTTRPDIGSPFIAQVNGVQMTLQIEPMGRFAFNGNDGNINGDEDDEDASERRII RIYYAALNDYKGTYSQSRNCERAKNLLELTYKEFQPHVDNLDPLQVFYYVRCLQLLGHMYFTGEGSSKPNIHMAEEILTT SLEISRRAQGPIGRACIDLGLINQYITNNISQAISYYMKAMKTQANNGIVEFQLSKLATSFPEEKIGDPFNLMETAYLNG FIPAIYEFAVMIESGMNSKSSVENTAYLFKTFVDKNEAIMAPKLRTAFAALINDRSEVALWAYSQLAEQGYETAQVSAAY LMYQLPYEFEDPPRTTDQRKTLAISYYTRAFKQGNIDAGVVAGDIYFQMQNYSKAMALYQGAALKYSIQAIWNLGYMHEH GLGVNRDFHLAKRYYDQVSEHDHRFYLASKLSVLKLHLKSWLTWITREKVNYWKPSSPLNPNEDTQHSKTSWYKQLTKIL QRMRHKEDSDKAAEDSHKHRTVVQNGANHRGDDQEEASEILGFQMEDGGGENLYFQSGGGMDEKTTGWRGGHVVEGLAGE LEQLRARLEHHPQGQREP Q05787 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 3 NAG singleParticle particle 0.8 7.5 Quantifoil R1.2/1.3 COPPER 400 GLOW DISCHARGE AIR ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 82.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION
projection matching from Guassian distritution
 C1 3.9 FSC 0.143 CUT-OFF RELION 1.4 204578 PROJECTION MATCHING PROJECTION MATCHING emd_8642.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 -192 -192 0 192 192 192 259.2 259.2 259.2 90.0 90.0 90.0 X Y Z -0.16199706 0.28196177 -0.000081890175 0.008258456 1.35 1.35 1.35 0.074 AUTHOR CryoEM map of Hrd3 filtering to 3.9A and applied with -180 b-factor emd_8642_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 -192 -192 0 192 192 192 259.2 259.2 259.2 90.0 90.0 90.0 X Y Z -0.04934124 0.11406551 -0.000081890175 0.00442448 1.35 1.35 1.35 AUTHOR CryoEM map of Hrd3 without filtering or amplitude modification