Cryo-EM structure of Rhizobium etli MprF

2026-08-05 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY em_admin em_imaging em_software entity entity_src_gen _chem_comp.name _chem_comp.pdbx_synonyms _em_admin.last_update _em_imaging.microscope_model _em_imaging.nominal_defocus_max _em_imaging.nominal_defocus_min _em_software.category _em_software.fitting_id _em_software.image_processing_id _em_software.name _em_software.version _entity.details _entity.formula_weight _entity.pdbx_description _entity.pdbx_number_of_molecules _entity_src_gen.pdbx_gene_src_scientific_name REFINEMENT_DESCRIPTION chem_comp_atom chem_comp_bond em_3d_fitting_list pdbx_initial_refinement_model refine _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 _refine.ls_d_res_high _refine.ls_d_res_low COORDINATE_REPLACEMENT AUTHOR Ligand identity

In the original deposition, the ligand was modeled as 1K1 (a covalently linked Lys-PGW molecule). The chemical structure of this ligand molecule was incorrect due to an erroneous bond assignment. The model has been corrected by replacing 1K1 with Lys and PGW components, and the original 1K1 definition should be deprecated.

STRUCTURE_SUMMARY atom_site audit_author chem_comp chem_comp_atom chem_comp_bond em_admin em_imaging em_software entity entity_src_gen pdbx_audit_support pdbx_contact_author pdbx_entity_instance_feature pdbx_entity_nonpoly pdbx_entry_details pdbx_nonpoly_scheme pdbx_struct_assembly_gen pdbx_struct_oper_list pdbx_struct_sheet_hbond pdbx_validate_torsion refine refine_ls_restr refine_ls_shell software struct_asym struct_conf struct_conn struct_ncs_oper struct_sheet struct_sheet_order struct_sheet_range _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _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.occupancy _atom_site.type_symbol _audit_author.name _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.type _em_admin.last_update _em_imaging.microscope_model _em_imaging.nominal_defocus_max _em_imaging.nominal_defocus_min _em_software.category _em_software.fitting_id _em_software.image_processing_id _em_software.name _em_software.version _entity.details _entity.formula_weight _entity.pdbx_description _entity.pdbx_number_of_molecules _entity_src_gen.pdbx_gene_src_scientific_name _pdbx_entity_nonpoly.comp_id _pdbx_entity_nonpoly.name _pdbx_entry_details.has_protein_modification _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi _struct_ncs_oper.matrix[1][1] _struct_ncs_oper.matrix[1][2] _struct_ncs_oper.matrix[1][3] _struct_ncs_oper.matrix[2][1] _struct_ncs_oper.matrix[2][2] _struct_ncs_oper.matrix[2][3] _struct_ncs_oper.matrix[3][1] _struct_ncs_oper.matrix[3][2] _struct_ncs_oper.matrix[3][3] _struct_ncs_oper.vector[1] _struct_ncs_oper.vector[2] _struct_ncs_oper.vector[3] PDBj PDBj 2021-06-17 2022-06-22 2022-06-22 2026-08-05 Japan Science and Technology JPMJCR20E2 Japan National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) 5R21AI144481-02 United States Japan Society for the Promotion of Science (JSPS) 20H03216 Japan Cryo-EM structure of Rhizobium etli MprF Nishimura M Hirano H flippase, aminoacyl-tRNA, phosphatidylglycerol, MEMBRANE PROTEIN Nishimura M Cryo-EM structure of Rhizobium etli MprF To Be Published 0353 7f47 FULLOVERLAP EMDB EMD-31445 associated EM volume

MprF MprF 0 1 Rhizobium etli CFN 42 0.187 Hypothetical conserved protein Rhizobium etli CFN 42 0.093918508

Sequence refers to NCBI Protein database (IPG: 15109202)

1 Escherichia coli BL21(DE3) LEVO MSGHGNLEEMEATDGFSFRTLFRRYRTPLTAAATLIVFCLVGYAIMQLTNEVRYDDVVAALAATGPSAILLALFFTALSF LSLVFYDLNAIEYIGKKLPFPHVALTAFSAYAVGNTAGFGALSGGAIRYRAYTRLGLSPEDIGRIIAFVTLSFGLGLAAV ASIALIIIASEIGPLIGVSPFLLRLIAGSIIAILGAVMIIGREGRVLNFGAVAIRLPDSRTWSRQFLVTAFDIAASASVL YVLLPQTAIGWPVFLAVYAIAVGLGVLSHVPAGLGVFETVIIASLGSAVNIDAVLGSLVLYRLIYHVLPLLIAVLAVSAA ELRRFVDHPAASSVRRIGGRLMPQLLSTLALLLGVMLVFSSVTPTPDQNLEFLSNYLPLPMVEGAHFLSSLLGLALVVAA RGLGQRLDGAWWVAVFSAVAALTLSLLKAIALVEAAFLAFLIFGLFVSRRLFTRHASLLNQAMTASWLMAIAVIVVGAVV ILLFVYRDVEYSNELWWQFEFTAEAPRGLRALLGITIISSAIAIFSLLRPATFRPEPATEEALTRAVEIVRKQGNADANL VRMGDKSIMFSEKGDAFIMYGRQGRSWIALFDPVGDHGAVQELVWRFVEAARAAGCRAVFYQISPALLSHCADAGLRAFK LGELAVADLRTFEMKGGKWANLRQTASRAQRDGLEFAVVEPENVPDIIDELAAVSTAWLEHHNAKEKGFSLGSFDPDYVS AQPVGILKKDGKIVAFANILVTESKEEGTIDLMRFSPDAPKGSMDFLFVQIMEYLRNQGFTHFNLGMAPLSGMSKREAAP VWDRIGSTVFEHGERFYNFKGLRAFKSKFHPHWQPRYLAVSGGGNPMIALMDATFLIGGGLKGVVRK Q2K4J4 (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate 0.0007490069999999999 2 PGW LYSINE 0.00014719499999999998 1 LYS water 1.8015e-05 4 HOH singleParticle particle 6 8.0 20.0 C4H11NO3-HCl Tris-HCl 150.0 NaCl sodium chloride 0.06 C56H92O25 GDN 100.0 C9H15O6P TCEP Quantifoil R1.2/1.3 GOLD 300 CARBON HOLEY ARRAY GLOW DISCHARGE 120 AIR ETHANE 100 277 FEI VITROBOT MARK IV

a waiting time of 10 s and a blotting time of 4 s.

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.8 1.6 GIF Bioquantum

CDS mode

GATAN K3 BIOQUANTUM (6k x 4k) 1 3159 5.0 56.0 1 CTFFIND PHASE FLIPPING AND AMPLITUDE CORRECTION C2 2.99 FSC 0.143 CUT-OFF RELION 3.1 307241 MAXIMUM LIKELIHOOD RELION 3.1 MAXIMUM LIKELIHOOD RELION 3.1 RELION 3.1 emd_31445.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 194 194 194 0 0 0 194 194 194 193.224 193.224 193.224 90.0 90.0 90.0 X Y Z -0.0021232832 0.0032375494 0.00000054811767 0.00010953165 0.996 0.996 0.996 0.000299 AUTHOR ::::EMDATABANK.org::::EMD-31445:::: 3.0 A "Best map" by EMDA 5VRV PDB experimental model RECIPROCAL emd_31445_msk_1.map emd_31445_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 194 194 194 0 0 0 194 194 194 193.224 193.224 193.224 90.0 90.0 90.0 X Y Z -0.014870308 0.052037254 0.00069435564 0.00418136 0.996 0.996 0.996 AUTHOR ::::EMDATABANK.org::::EMD-31445:::: emd_31445_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 194 194 194 0 0 0 194 194 194 193.224 193.224 193.224 90.0 90.0 90.0 X Y Z -0.014699429 0.051593807 0.0006962131 0.004181944 0.996 0.996 0.996 AUTHOR ::::EMDATABANK.org::::EMD-31445::::