2026-08-12 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY REFINEMENT_DESCRIPTION em_3d_fitting_list em_admin pdbx_initial_refinement_model _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 STRUCTURE_SUMMARY em_admin entity _em_admin.last_update _entity.formula_weight 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 pdbx_validate_close_contact struct_conn _chem_comp.formula _chem_comp.formula_weight _em_admin.last_update _entity.formula_weight PDBj PDBj 2022-05-30 2022-11-16 2022-11-16 2026-08-12 Japan Agency for Medical Research and Development (AMED) JP21am0101118 Japan Japan Agency for Medical Research and Development (AMED) JP21am0101116 Japan Japan Society for the Promotion of Science (JSPS) JP16H04174 Japan Japan Society for the Promotion of Science (JSPS) JP18H05153 Japan Japan Society for the Promotion of Science (JSPS) 20H05086 Japan Japan Society for the Promotion of Science (JSPS) 20H02856 Japan Tani K Kanno R Kurosawa K Takaichi S Nagashima KVP Hall M Yu L-J Kimura Y Madigan MT Mizoguchi A Humbel BM Wang-Otomo Z-Y LH1-RC COMPLEX, PHOTOSYNTHESIS, PURPLE BACTERIA Tani K Kanno R Kurosawa K Takaichi S Nagashima KVP Hall M Yu LJ Kimura Y Madigan MT Mizoguchi A Humbel BM Wang-Otomo ZY Commun Biol UK 5 1197 1197 2022 36344631 doi:10.1038/s42003-022-04174-2 2399-3642 Tani K Kanno R Kurosawa K Takaichi S Nagashima KVP Hall M Yu L-J Kimura Y Madigan MT Mizoguchi A Humbel BM Wang-Otomo Z-Y Commun Biol UK 5 2022 doi:10.1038/s42003-022-04 2399-3642 7xxf FULLOVERLAP EMDB EMD-33501 associated EM volume

STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF Rhodopila globiformis

Photosynthetic LH1-RC complex from the purple phototrophic bacterium Rhodopila globiformis Photosynthetic LH1-RC complex from the purple phototrophic bacterium Rhodopila globiformis 0 1 2 3 4 5 6 7 Rhodopila globiformis 0.4 Photosynthetic reaction center cytochrome c subunit Rhodopila globiformis 0.037945188 1 LEVO MNTGVQAALAAAAVAAVAVAGVVFGTFERPPIETVQRGARGLAMSELYNPRFLAETRAENVVPASLPRLPDVGLKAGEVY HNVQVLKDVSVGNFTRLMASMTTWVAPQQGCGYCHNTNNMASDAKYTKVVARRMIQMVQHINQDWKVHVMANAPTGVVCY TCHRGNPVPKNIWFNNPGPLQAGGYAEAEIGKNHPAPFANNSSLPLDPFTPFLEHAENIRVQATQALPGTDNSSIKQTYW TYALMASFTQALGVNCTYCHDSRLWESWDMAPPQRVTAWYGIRMVRDLNNNFLDPLKTTFPDYRRGPLGDSPKVWCATCH NGVYKPLFGKSMVTTFPELTKVSQ A0A2S6NEK5 Reaction center protein L chain Rhodopila globiformis 0.030697745999999998 1 LEVO MAMLSFEPKYRTRGGTLIGGDLFDFWVGPLWVGFFGVTAAFFAILGTLLIVWAAALGPTWNIWRINIAPPDISYGLAFAP LREGGLWQLITVCACGAFVSWALRQVEIARKLGMGLHIPFAFSFAILAYFTLVVFRPLLMGAWGYGFPYGILSHLDWVSN TGYQYLHFHYNPAHMIAISFFFTNALALALHGSLILSAANPPKGEVVKGAEQENGYFRDVIGYSIGTLGIHRLGVFLAVS AAFWSAVCIIISGPFWTRGWPEWWSWWLNLPMWSH A0A2S6NEG7 Reaction center protein M chain Rhodopila globiformis 0.036345332 1 LEVO MPEFQNVFTRVQVKGPVHMGVPLPRGSWARTGKPFHLYLLGLIGDAQIGPIYLGFSGVASIIFGFIAIEIIGFNMLASVD WSVPEFFRQFFWLALEPPAPKYGLGLAPLAEGGWWGMAGFFLTASILLWWVRMYRRARALGLGTHTAWAFASAIFLYLSL GFIRPILMGCWCEAPPFGIFPHLDWTAAFSLRYGNLFYNPFHMLSIAFLYGSAVLFAMHGGTVLATTRFGGEREVEQITD RGTAGERAMLFWRWTMGFNATFESIHRWGWWFAVLVTLTGGIGILLTGTVVDNWFLWGVKHGIAAPWPNVFPHVVDPALL ATGVGK A0A2S6NEP5 Photosynthetic reaction center H subunit Rhodopila globiformis 0.028383366999999996 1 LEVO MEIGAITQQIDAAQLVLYTFWLFFAGLIIYLRMEDKREGYPLVTEIPGKFLEGFPPMPAPKTFILTHNQGTVTVPRAVPR AEIEYKAEPCAAWPGAPHEPVGPNKMLSGAGPSGYALRFDTPEPTFDTGVPRMAPMRVATDHVFDEDGPNPIGYDLVGFD GIVAGKITDAWVDREESLVRYLEAKLTNDKSILVPMPLSRVKDSTGQVLLASLKGEQVLEAPTLANPDQVTLREEDRIAA YFASGHLYATQARQESIL A0A2S6MZS1 Light-harvesting protein Rhodopila globiformis 0.007048523 16 LEVO (FME)WRMWLLFDPRRILVALGVFLFVLALLIHFILLSTDRFNWLDGPHRGAVAAQMAPLPAPVK A0A2S6NEK3 Light-harvesting protein Rhodopila globiformis 0.007877074999999999 16 LEVO MTPGGPSITGLTEAEAKEFHGIFITSFIVFTVIAIVAHLLAWQWRPWLPAVTGYGTAMNDAVSFIHATISQLA A0A2S6NEL9 Light-harvesting protein LH1 Gamma-like Rhodopila globiformis 0.0025421989999999998 11 LEVO (FME)AMVWMWILIAPAIGIVLLSRQ 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 18 PGV BACTERIOCHLOROPHYLL A 0.0009115039999999999 36 BCL BACTERIOPHEOPHYTIN A 0.000889215 2 BPH UBIQUINONE-10 0.0008633429999999999 4 U10 DODECYL-BETA-D-MALTOSIDE 0.000510615 5 LMT FE (III) ION 5.5845e-05 1 FE MENAQUINONE-9 0.0007852329999999999 1 MQ9 (6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E},26~{E},28~{E})-2,31-dimethoxy-2,6,10,14,19,23,27,31-octamethyl-dotriaconta-6,8,10,12,14,16,18,20,22,24,26,28-dodecaen-5-one 0.0006129239999999999 17 I7D CARDIOLIPIN 0.0014640429999999997 9 CDL 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine 0.000744034 1 PEE water 1.8015e-05 538 HOH singleParticle particle 5.0 7.5 ETHANE 80 277 LEICA EM GP

This sample was monodisperse.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.6 2.8000000000000003 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON III (4k x 4k) COUNTING 38.9 40.0 1 CTFFIND PHASE FLIPPING ONLY FOURIER SPACE 2.24 FSC 0.143 CUT-OFF RELION 3.1 128119 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD RELION 3.1 RELION 3.1 5Y5S PDB experimental model RIGID BODY FIT Correlation coefficient REAL 40.0 emd_33501_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 328.0 328.0 328.0 90.0 90.0 90.0 X Y Z -0.04288069 0.15635873 0.000089126566 0.0045529716 0.82 0.82 0.82 AUTHOR ::::EMDATABANK.org::::EMD-33501:::: half map of even number emd_33501_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 328.0 328.0 328.0 90.0 90.0 90.0 X Y Z -0.04206364 0.16283238 0.00009238095 0.004551496 0.82 0.82 0.82 AUTHOR ::::EMDATABANK.org::::EMD-33501:::: half map of odd number