Cryo-EM structure of native RC-LH complex from Roseiflexus castenholzii at 100lux

2026-09-30 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update STRUCTURE_SUMMARY em_admin entity _chem_comp.name _chem_comp.pdbx_synonyms _em_admin.last_update _entity.formula_weight _entity.pdbx_description REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY em_admin pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order pdbx_struct_conn_angle struct_conn _em_admin.last_update STRUCTURE_SUMMARY atom_site chem_comp chem_comp_atom chem_comp_bond em_admin entity pdbx_entity_nonpoly pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order pdbx_nonpoly_scheme pdbx_struct_conn_angle pdbx_validate_chiral struct_conn _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.label_atom_id _atom_site.label_comp_id _atom_site.type_symbol _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.name _chem_comp.pdbx_synonyms _em_admin.last_update _entity.formula_weight _entity.pdbx_description _pdbx_entity_nonpoly.comp_id _pdbx_entity_nonpoly.name _pdbx_modification_feature.auth_comp_id _pdbx_modification_feature.label_comp_id _pdbx_modification_feature.ref_comp_id _pdbx_modification_feature.ref_pcm_id _pdbx_nonpoly_atom_coordination.auth_comp_id _pdbx_nonpoly_atom_coordination.label_comp_id _pdbx_nonpoly_atom_coordination_sphere.auth_comp_id _pdbx_nonpoly_atom_coordination_sphere.label_comp_id _pdbx_nonpoly_atom_coordination_sphere_order.auth_comp_id _pdbx_nonpoly_atom_coordination_sphere_order.label_comp_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_label_comp_id PDBj PDBj 2023-04-24 2023-09-20 2023-09-20 2026-09-30 National Natural Science Foundation of China (NSFC) China Cryo-EM structure of native RC-LH complex from Roseiflexus castenholzii at 100lux Xu X Xin J RC-LH core complex, PHOTOSYNTHESIS Xin J Shi Y Zhang X Yuan X Xin Y He H Shen J Blankenship RE Xu X Carotenoid assembly regulates quinone diffusion and the Roseiflexus castenholzii reaction center-light harvesting complex architecture. Elife US 12 2023 37737710 doi:10.7554/eLife.88951 2050-084X 8j5o FULLOVERLAP EMDB EMD-35988 associated EM volume

the native RC-LH complex at 100lux the native RC-LH complex at 100lux 0 1 2 3 4 5 6 7 8 Roseiflexus castenholzii DSM 13941 Beta subunit of light-harvesting 1 Roseiflexus castenholzii DSM 13941 0.006431528 15 LEVO MTDKPQNDLVPDQWKPLFNNAQWLVHDIVVKTIYGGLIIAVIAHVLCWAWTPWIR Q83XD2 Alpha subunit of light-harvesting 1 Roseiflexus castenholzii DSM 13941 0.004724656 15 LEVO MKDRPFEFRTSVVVSTLLGLVMALLIHFVVLSSGAFNWLRAP Q83XD1 MULTIHEME_CYTC DOMAIN-CONTAINING PROTEIN Roseiflexus castenholzii DSM 13941 0.034923031 1 LEVO MIQQPPTLFPEITNTVRGRFYIVAGIISVVMAVASIAIFWWIFYTITPAPAPPLQNPIYVNYTQEPTDYISAESLAAMNA YIQANPQPQAVQVLKGMTTAQISAYMVAQVSGGLKVDCSYCHNIANFAQQDGYPNAAKKVTARKMMLMSADLNQNYTAKL PASVGGYQITCATCHNGKAAGLEPYPIEIMNTLPNDWRLPLELDYPGGLVVTGRKDVSNHEVEQNQFAMYHMNVSMGQGC TFCHNARYFPSYEIAQKNHSIIMLQMTKHIQETYVAPGGRIADGIMAGKSPSCWLCHQGANIPPGAAKPGQVPAVLSSTP A7NQE7 Reaction center protein L chain Roseiflexus castenholzii DSM 13941 0.034844230000000004

The L- and M-subunits of the RC are encoded by a fused gene pufLM but post-translational processed into two discrete subunits each containing six and five transmembrane helices

1 LEVO MSAVPRALPLPSGETLPAEAISSTGSQAASAEVIPFSIIEEFYKRPGKTLAARFFGVDPFDFWIGRFYVGLFGAISIIGI ILGVAFYLYEGVVNEGTLNILAMRIEPPPVSQGLNVDPAQPGFFWFLTMVAATIAFVGWLLRQIDISLKLDMGMEVPIAF GAVVSSWITLQWLRPIAMGAWGHGFPLGITHHLDWVSNIGYQYYNFFYNPFHAIGITLLFASTLFLHMHGSAVLSEAKRN ISDQNIHVFWRNILGYSIGEIGIHRVAFWTGAASVLFSNLCIFLSGTFVKDWNAFWGFWDKMPIWNGVGQGALVA A7NQE8 Reaction center protein M chain Roseiflexus castenholzii DSM 13941 0.035046078

The L- and M-subunits of the RC are encoded by a fused gene pufLM but post-translational processed into two discrete subunits each containing six and five transmembrane helices

1 LEVO PIDLHDEEYRDGLEGTIAKPPGHVGWMQRLLGEGQVGPIYVGLWGVISFITFFASAFIILVDYGRQVGWNPIIYLREFWN LAVYPPPTEYGLSWNVPWDKGGAWLAATFFLHISVLTWWARLYTRAKATGVGTQLAWGFASALSLYFVIYLFHPLALGNW SAAPGHGFRAILDWTNYVSIHWGNFYYNPFHMLSIFFLLGSTLLLAMHGATIVATSKWKSEMEFTEMMAEGPGTQRAQLF WRWVMGWNANSYNIHIWAWWFAAFTAITGAIGLFLSGTLVPDWYAWGETAKIVAPWPNPDWAQYVFR A7NQE8 Subunit X Roseiflexus castenholzii DSM 13941 0.0036284769999999997 1 LEVO MAPFLMAFFTIVLIVATLYFLSMIMSGKPESR Subunit Y Roseiflexus castenholzii DSM 13941 0.004493262 1 LEVO MNWIVATFMLMFVLVAFLPLVVSLAYTWVTNPETQSTEE Subunit Z Roseiflexus castenholzii DSM 13941 0.006927004 1 LEVO MDFLILLQAEPSPWPVWSGYALCFVPLAAVILGFIIAARFTDKQATSAYLRLDPAKANEPEQG BACTERIOCHLOROPHYLL A 0.0009115039999999999 48 BCL beta,psi-caroten-4-one 0.000550856 30 KGD HEME C 0.0006205189999999999 4 HEC (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE 0.0007490069999999999 4 PGV BACTERIOPHEOPHYTIN A 0.000889215 3 BPH FE (III) ION 5.5845e-05 1 FE 2-methyl-3-[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,1 4,18,22,26,30,34,38,42-undecaen-1-yl]naphthalene-1,4-dione 0.0009214669999999999 3 MQE singleParticle particle 8.0 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.2 2.0 GATAN K3 (6k x 4k) 50.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 2.9 FSC 0.143 CUT-OFF 322595 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_35988.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 264 264 264 0 0 0 264 264 264 235.752 235.752 235.752 90.0 90.0 90.0 X Y Z -0.12581758 0.23744218 0.0002489091 0.008848198 0.893 0.893 0.893 0.02 AUTHOR ::::EMDATABANK.org::::EMD-35988:::: emd_35988_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 264 264 264 0 0 0 264 264 264 235.752 235.752 235.752 90.0 90.0 90.0 X Y Z -0.027774481 0.06277782 0.00024934436 0.003787357 0.893 0.893 0.893 AUTHOR ::::EMDATABANK.org::::EMD-35988:::: emd_35988_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 264 264 264 0 0 0 264 264 264 235.752 235.752 235.752 90.0 90.0 90.0 X Y Z -0.02633224 0.064095214 0.00024847387 0.0037786488 0.893 0.893 0.893 AUTHOR ::::EMDATABANK.org::::EMD-35988::::