Cryo-EM structure of Bimetallic dodecameric cage design 3 (BMC3) from cytochrome cb562

2026-08-12 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY em_admin entity _em_admin.last_update _entity.formula_weight DATABASE_REFERENCES citation _citation.journal_volume _citation.page_first _citation.page_last STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond database_2 em_3d_fitting_list em_admin pdbx_entry_details pdbx_initial_refinement_model pdbx_modification_feature pdbx_struct_conn_angle struct_conn struct_conn_type _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_3d_fitting_list.accession_code _em_3d_fitting_list.initial_refinement_model_id _em_3d_fitting_list.source_name _em_3d_fitting_list.type _em_admin.last_update _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.conn_type_id _struct_conn.id _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn_type.id REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY chem_comp chem_comp_atom chem_comp_bond em_admin entity pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order pdbx_struct_conn_angle pdbx_validate_chiral struct_conn _chem_comp.formula _chem_comp.formula_weight _em_admin.last_update _entity.formula_weight RCSB RCSB 2019-05-07 2020-01-29 2020-01-29 2026-08-12 National Science Foundation (NSF, United States) DMR-1602537 United States Department of Energy (DOE, United States) DE-SC0003844 United States European Molecular Biology Organization (EMBO) ALTF 1336-2015 European Union German Research Foundation (DFG) 393131496 Germany Cryo-EM structure of Bimetallic dodecameric cage design 3 (BMC3) from cytochrome cb562 Golub E Subramanian RH Supramolecular assembly, protein cage, bimetallic, metal binding, hydroxamic acid, METAL BINDING PROTEIN Golub E Subramanian RH Esselborn J Alberstein RG Bailey JB Chiong JA Yan X Booth T Baker TS Tezcan FA Constructing protein polyhedra via orthogonal chemical interactions. Nature UK 578 172 176 2020 31969701 doi:10.1038/s41586-019-1928-2 1476-4687 0006 NATUAS 6ovh FULLOVERLAP EMDB EMD-20212 associated EM volume

Bimetallic dodecameric cage 3 (BMC3) Bimetallic dodecameric cage 3 (BMC3) 0 1

Cryo-EM reconstruction of self-assembled BMC3 dodecameric cages

Escherichia coli 0.15 Soluble cytochrome b562 Escherichia coli 0.011809307 12 Escherichia coli BL21(DE3) LEVO ADLEHNMHTLNDNLKHIEKADNATTVKDALTKMQAAAQDAWSATPPKLEDKSPDSPEMSDFRCGFWELIGQINAALHLAK QCKVKEAQAAAEQLKTTCNACHQKYR P0ABE7 HEME C 0.0006205189999999999 12 HEC ACETOHYDROXAMIC ACID 7.506699999999999e-05 24 HAE ZINC ION 6.5409e-05 24 ZN FE (III) ION 5.5845e-05 8 FE water 1.8015e-05 171 HOH singleParticle particle 8.5 20.0 Tris Quantifoil R1.2/1.3 COPPER 400 GLOW DISCHARGE 30 AIR 101.325

The grid was glow discharged at 20 mA for 30 s.

ETHANE FEI VITROBOT MARK IV

Protein solutions containing 20 micromolar BMC3 in 20 mM Tris (pH 8.5) were incubated with [FeSO4] = 20 micromolar, [ZnCl2] = 60 micromolar for 2-3 h to form cages. Samples were concentrated 10 fold prior to grid preparation.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) 4672 10.0 60.0 1 805156 NONE 6OT7 T 2.6 FSC 0.143 CUT-OFF 25391 NOT APPLICABLE NOT APPLICABLE emd_20212.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 216.3712 216.3712 216.3712 90.0 90.0 90.0 X Y Z -0.10569239 0.17277433 0.00025228798 0.005550816 0.8452 0.8452 0.8452 0.026 AUTHOR ::::EMDATABANK.org::::EMD-20212:::: 2.6 A map of dodecameric cage 6OT7 PDB experimental model RIGID BODY FIT

Symmetry mates were generated from the atomic model to build the dodecameric cage. Chain IDs were re-assigned to ascend from A-L. The cage PDB was manually fit to the EM density map in UCSF Chimera and refined using phenix.real_space_refine

REAL emd_20212_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 216.3712 216.3712 216.3712 90.0 90.0 90.0 X Y Z -0.017495759 0.060654353 0.00017038624 0.0024471236 0.8452 0.8452 0.8452 AUTHOR ::::EMDATABANK.org::::EMD-20212:::: half-map 1 prior to postprocessing in Relion 3.0 emd_20212_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 216.3712 216.3712 216.3712 90.0 90.0 90.0 X Y Z -0.018630447 0.060713727 0.00016826975 0.0024491167 0.8452 0.8452 0.8452 AUTHOR ::::EMDATABANK.org::::EMD-20212:::: half-map 2 prior to postprocessing in Relion 3.0