2026-08-12 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update STRUCTURE_SUMMARY em_admin pdbx_entry_details pdbx_modification_feature _em_admin.last_update _pdbx_entry_details.has_protein_modification 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 pdbx_validate_close_contact struct_conn _em_admin.last_update PDBj PDBj 2023-09-16 2024-02-21 2024-02-21 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 Photosynthetic LH1-RC complex from the purple sulfur bacterium Allochromatium vinosum purified by sucrose density Tani K Kanno R Harada A Kobayashi A Minamino A Nakamura N Ji X-C Purba ER Hall M Yu L-J Madigan MT Mizoguchi A Iwasaki K Humbel BM Kimura Y Wang-Otomo Z-Y PHOTOSYNTHESIS Tani K Kanno R Harada A Kobayashi Y Minamino A Takenaka S Nakamura N Ji XC Purba ER Hall M Yu LJ Madigan MT Mizoguchi A Iwasaki K Humbel BM Kimura Y Wang-Otomo ZY High-resolution structure and biochemical properties of the LH1-RC photocomplex from the model purple sulfur bacterium, Allochromatium vinosum. Commun Biol UK 7 176 176 2024 38347078 doi:10.1038/s42003-024-05863-w 2399-3642 8wdu FULLOVERLAP EMDB EMD-37465 associated EM volume
Photosynthetic LH1-RC complex from the purple sulfur bacterium Allochromatium vinosum purified by sucrose density
 Photosynthetic LH1-RC complex from the purple sulfur phototrophic bacterium Allochromatium vinosum Photosynthetic LH1-RC complex from the purple sulfur phototrophic bacterium Allochromatium vinosum 0 1 2 3 4 5 6 7 8 9 Allochromatium vinosum DSM 180 Photosynthetic reaction center cytochrome c subunit Allochromatium vinosum DSM 180 0.041512555 1 LEVO MNLGKQLTLPAVAVVASVVLLGCERPPPEVVQKGYRGVAMEQNYNPRLLEASIKANLPVESLPAAAPGGPSVSDVYENVQ VLKDLSVAEFTRTMVAVTTWVAPKEGCNYCHVPGNWASDDIYTKVVSRRMFELVRATNSNWKDHVAETGVTCYTCHRGNP VPKYVWVTDPGPNQPSGVTPTGQNYASSTVAYSALPLDPYTPFLDQSNEIRVIGQTALPAGNTTSLKQAEWTYGLMMQIS DSLGVNCTFCHNSRSFYDWKQSTPQRTTAWYAIRHVRDINQNYIWPLNDALPASRKGPYGDPFKVGCMTCHQGAYKPLYG AQMAKDYPALYESAPAEAAPATEEAPAAEAEAVEAAPVEEAAPAPVEQAAAPVEDAAPAPQQL O82947 Reaction center protein L chain Allochromatium vinosum DSM 180 0.031217409999999998 1 LEVO MAMLSFERKYRVRGGTLIGGDLFDFWVGPFYVGFFGVAGFFFALLGVLLIVWGATIGPNAELQTYNIWQISIAPPDLSYG LGMAPMTEGGLWQIITICAIGAFVSWALREVEICRKLGIGFHIPFAFAFAIGAYLVLVVVRPILMGAWGHGFPYGILSHL DWVSNVGYQFLHFHYNPAHMLAITFFFTNCLALSMHGSLILSVTNPQKGEEVKTSEHENTFFRDIVGYSIGALAIHRLGL FLALSAVFWSAVCIVISGPFWTRGWPEWWNWWLELPLW P51762 Reaction center protein M chain Allochromatium vinosum DSM 180 0.036364242 1 LEVO MPEYQNIFTTVQVRAPAYPGVPLPKGSLPRIGKPIFSYWAGKIGDAQIGPIYLGFTGTLSIIFGFMAIFIIGFNMLASVD WNIIQFVKHFFWLGLEPPAPQYGLTIPPLSEGGWWLMAGFFLTMSILLWWVRTYKRAEALGMSQHLSWAFAAAIFFYLSL GFIRPVMMGSWAEAVPFGIFPHLDWTAAFSIRYGNLYYNPFHMLSIAFLYGSALLFAMHGATILAVSRFGGDREIDQITD RGTAAERAAIFWRWTMGFNASMESIHRWAWWCAVLTVITAGIGILLTGTVVENWYLWAIKHGVAPAYPEVVTAVDPYATA TGVTQ P51763 Photosynthetic reaction center H subunit Allochromatium vinosum DSM 180 0.028231319999999997 1 LEVO (FME)SAAITEYMDVAQLTIWAFWFFFAGLIIYLRREDKREGYPLDSDRTERSGGRVKVVGFPDLAEPKTFVLPHNAGTV MAPRVEAPTSINATPVAPFPGAPFEPNGDPMLSGFGPSASPDRAKHCDLTFEGLPKIVPLRVATDFSIAERDPDPRGMTV VGLDGEVAGTVSDVWVDRSEPQIRYLEVKVAAGGKNVLLPIGFSRFDKKARKVKVAAIKAAHFANVPTLAKPDQITLYEE DKVCAYYAGGKLYATAERAGPLL D3RPF6 Antenna complex alpha/beta subunit Allochromatium vinosum DSM 180 0.005136131 9 LEVO (FME)HKIWQIFDPRRTLVALFGFLFVLGLLIHFILLSSPAFNWLSGS D3RP69 Antenna complex alpha/beta subunit Allochromatium vinosum DSM 180 0.005269103 10 LEVO MANSSMTGLTEQEAQEFHGIFVQSMTAFFGIVVIAHILAWLWRPWL D3RP75 Antenna complex alpha/beta subunit Allochromatium vinosum DSM 180 0.007244582999999999 6 LEVO (FME)SPDLWKIWLLVDPRRILIAVFAFLTVLGLAIHMILLSTAEFNWLEDGVPAATVQQVTPVVPQR D3RP74 Antenna complex alpha/beta subunit Allochromatium vinosum DSM 180 0.005518471999999999 6 LEVO MADQKSMTGLTEEEAKEFHGIFTQSMTMFFGIVIIAHILAWLWRPWL D3RP68 Antenna complex alpha/beta subunit Allochromatium vinosum DSM 180 DSM 180 0.007392856999999999 1 LEVO MMPQLYKIWLAFDPRMALIGLGAFLFALALFIHYMLLRSPEFDWLLGPDYAPVTLSAGMSALPAGR D3RP67 PROTOPORPHYRIN IX CONTAINING FE 0.000616487 4 HEM MAGNESIUM ION 2.4305e-05 1 MG (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate 0.000568911 1 Z41 PALMITIC ACID 0.00025642399999999994 1 PLM (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE 0.0007490069999999999 11 PGV BACTERIOCHLOROPHYLL A 0.0009115039999999999 36 BCL BACTERIOPHEOPHYTIN A 0.000889215 2 BPH Ubiquinone-8 0.000727109 3 UQ8 DODECYL-BETA-D-MALTOSIDE 0.000510615 22 LMT CARDIOLIPIN 0.0014640429999999997 5 CDL FE (III) ION 5.5845e-05 1 FE MENAQUINONE 8 0.000717116 1 MQ8 SPIRILLOXANTHIN 0.0005969249999999999 17 CRT CALCIUM ION 4.0078e-05 6 CA LAURYL DIMETHYLAMINE-N-OXIDE 0.00022940199999999997 2 LDA water 1.8015e-05 334 HOH singleParticle particle 4.0 8.0 ETHANE 90 277 LEICA EM GP
This sample was monodisperse.
 JEOL CRYO ARM 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.7000000000000001 3.2 JEOL NITROGEN GATAN K3 (6k x 4k) COUNTING 2.0 50.0 1 361654 CTFFIND PHASE FLIPPING ONLY 1 FOURIER SPACE 2.24 FSC 0.143 CUT-OFF RELION 3.1 252230 MAXIMUM LIKELIHOOD RELION 3.1 MAXIMUM LIKELIHOOD RELION 3.1 RELION 3.1 emd_37465.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 290.88 290.88 290.88 90.0 90.0 90.0 X Y Z -0.056558464 0.14307253 0.0000512537 0.003502972 0.606 0.606 0.606 0.013 AUTHOR Photosynthetic LH1-RC complex from the purple sulfur bacterium Allochromatium vinosum 7VRJ PDB experimental model RIGID BODY FIT Correlation coefficient REAL 44.0 emd_37465_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 290.88 290.88 290.88 90.0 90.0 90.0 X Y Z -0.027242456 0.06169271 0.000051126524 0.0026937563 0.606 0.606 0.606 AUTHOR Even half map emd_37465_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 290.88 290.88 290.88 90.0 90.0 90.0 X Y Z -0.027158093 0.06306656 0.000051380877 0.0026892633 0.606 0.606 0.606 AUTHOR Odd half map