2026-08-12 REL PDBc INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY em_admin entity _em_admin.last_update _entity.formula_weight DATABASE_REFERENCES citation citation_author em_admin _citation.page_first _citation.page_last _citation_author.identifier_ORCID _em_admin.last_update REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY chem_comp chem_comp_atom chem_comp_bond em_admin entity pdbx_entry_details 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 struct_conn_type _chem_comp.formula _chem_comp.formula_weight _em_admin.last_update _entity.formula_weight _pdbx_entry_details.has_protein_modification PDBj PDBc 2024-04-05 2025-04-02 2025-04-02 2026-08-12 National Natural Science Foundation of China (NSFC) 32100202 China Chen JH Zheng Q Zhang X Photosynthesis, Reaction center, Energy transfer, Photosynthetic bacteria Wang W Liu Y Gu J An S Ma C Gao H Jiao N Shen JR Beatty JT Koblizek M Zhang X Zheng Q Chen JH Adv Sci DE 12 e2413456 e2413456 2025 40112203 doi:10.1002/advs.202413456 2198-3844 8yz2 FULLOVERLAP EMDB EMD-39683 associated EM volume

Cryo-EM structure of a tri-heme cytochrome-associated RC-LH1 complex from a marine photoheterotrophic bacterium, purified with magnesium-free solutions.

tri-heme cytochrome-associated RC-LH1 complex tri-heme cytochrome-associated RC-LH1 complex 0 2 3 1 4 5 6 7 Dinoroseobacter shibae DFL 12 = DSM 16493 Antenna pigment protein alpha chain Dinoroseobacter shibae DFL 12 = DSM 16493 0.006195408999999999 17 LEVO MSKFYKIWLIFDPRRVFVAQGVFLFLLAAMIHLVLLSTEHFNWFELAAANAAM A8LQ15 Reaction center protein O chain Dinoroseobacter shibae DFL 12 = DSM 16493 0.025206586 1 LEVO MATQRKDMTCTITCWGIGVLLGIMTTVGLMVVGWSFLQGAFMGVLAWLIVGGVLAVAVCGETGRPKDNAEQIRAEMAAAR ERVRGATPGITPKPAPSVPADVRSKVQPSAALAGEAELAGRKGSWSYDSGAGHASGAGHDAGTDAAKPATLTAARDGKAD DLKKIKGVGPKLEEMLHSMGFYHFDQVASWSEQELAWVDENLEGFKGRASRDEWVAQAKLLAQGGETEFSKRVDGGDVY A8LIU2 Antenna pigment protein beta chain Dinoroseobacter shibae DFL 12 = DSM 16493 0.005578334 17 LEVO MADKSDLSFTGLTDEQAQELHSVYMSGLWLFSAVAVVAHLATFIWRPWF A8LQ14 Reaction center protein M chain Dinoroseobacter shibae DFL 12 = DSM 16493 0.037583723 1 LEVO MPEYQNIFTQVQVQGPAELGVDNENNLTEERTTGTGFSQLIGWIGNAQLGPIYLGWFGIISLVTGTLWFNIVGFNMLSQV GYSIPEFIRQLFWLALEPPSPEYGLRMPPLDDGGWFIIASFFLLVSVISWWLRSYQLAEMHKMGKHVAWAFAAAIWLFLV LGLFRPILMGSWSEAVPYGIFPHLDWTTAFSIRYGNLYYNPFHALSIVFLYGSVLLFAMHGATILAVTRFGGDRELEQIY DRGTASERAGLFWRWTMGFNATMEGIHRWAWWFAVLTPITGGIGILLTGTVVDNWFLWAVEHNFAPDYTQDYGYEAYTTY DGFLGREEGN A8LQ17 Reaction center protein L chain Dinoroseobacter shibae DFL 12 = DSM 16493 0.031197178 1 LEVO MALLSFERKYRVRGGTLIGGDLFDFWVGPFYVGFFGVTTAFFALLGTILIFWGASQQGTFNPWLINIAPPDLSYGLGMAP LMEGGLWQIITICAIGAFVSWALREVEICRKLGMGYHVPFAFSVAIFAYVTLVVFRPLLMGAWGHGFPYGIWSHLDWVSN TGYAYLHFHYNPAHMIAVTFFFTTTLALALHGALVLSAANPPKGEEVKGPDNEDTFFRDFIGYSIGTLGIHRVGLLLALN AGFWSAVCIIISGPVWTKGWPEWWNWWLEMPIWPSQVDC A8LQ16 Reaction center protein H chain Dinoroseobacter shibae DFL 12 = DSM 16493 0.028739449 1 LEVO MEETFFGNFDLASLSLWLFYGFFALLIYYLQTENMREGYPLEDDDGNTAANQGPFPLPKEKTFKLQHGRGELTLPGEDVQ RRDNLALRKTAHGNGFPMEPTGDPMLDGVGPASWSKRRDVPELDAHGHPKIVPMSAAEGFGVSAGTDPRGLPVMAGDGEI VGLVSDMWIDEAEQLVRYLEIELDPEWGDGKRLVQREMVRIKSDRVKVRSIYGKHFKNVPKTKSPNQVTLLEEDKIMAYY AGGTLYADESRLEPQL A8LQ33 Photosynthetic reaction center cytochrome c subunit Dinoroseobacter shibae DFL 12 = DSM 16493 0.039977367 1 LEVO MLPKWFDEWNSKNPTDIYKPAIVVGVAGGAVFAAALLVSWGQPLATDSMQTGPRGTGMSVPEFVSDLDTPDPTIEVFLAS TSDPVIPEEGAQTAGEAYENVDPVLADLTVENYDRLLAAMRSWTGIPDLLEDPDHYQSKVAINMIQMNQTINEEWAGHVY ANAEVGVTCFTCHRGQAVPSEVWYRIDPVTENTSGWASVQNRATSLSQFTSLPSDALYQYLLNYEQIAVHDLESRVETLP GDPTWQNTERTYSLMNYFSNSLGRNCVFCHNSRAFYDPAQHTPQWATAMLGISMVQELNNEWIVPIGEAHLPPERLGPVY NDVPKLACKTCHKGYQQPLQGLNVVADWPELATTEGPFYD A8LQ18 BACTERIOCHLOROPHYLL A 0.0009115039999999999 38 BCL (4~{E},16~{E},26~{E})-2-methoxy-2,6,10,14,19,23,27,31-octamethyl-dotriaconta-4,6,8,10,12,14,16,18,20,22,26,30-dodecaen-3-one 0.000582898 35 A1EFU (21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaoctacosan-21-yl (9Z)-octadec-9-enoate 0.0007770599999999999 12 MW9 FE (III) ION 5.5845e-05 1 FE UBIQUINONE-10 0.0008633429999999999 2 U10 DODECYL-BETA-D-MALTOSIDE 0.000510615 5 LMT BACTERIOPHEOPHYTIN A 0.000889215 2 BPH CARDIOLIPIN 0.0014640429999999997 2 CDL HEME C 0.0006205189999999999 3 HEC singleParticle particle 8.0 ETHANE 100 279 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.5 2.5 FEI FALCON IV (4k x 4k) 50.0 1 cryoSPARC 4.2.1 PHASE FLIPPING AND AMPLITUDE CORRECTION C1 2.68 FSC 0.143 CUT-OFF cryoSPARC 4.2.1 194156 MAXIMUM LIKELIHOOD cryoSPARC 4.2.1 MAXIMUM LIKELIHOOD cryoSPARC 4.2.1 10 cryoSPARC 4.2.1 emd_39683_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 238.08 238.08 238.08 90.0 90.0 90.0 X Y Z -0.678993 0.8307176 0.0012686057 0.07598426 0.93 0.93 0.93 AUTHOR ::::EMDATABANK.org::::EMD-39683:::: Cryo-EM structure of a tri-heme cytochrome-associated RC-LH1 complex from a marine photoheterotrophic bacterium, purified with magnesium-containing solutions-half-map-B emd_39683_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 238.08 238.08 238.08 90.0 90.0 90.0 X Y Z -0.52850616 0.80143297 0.0012758984 0.07605743 0.93 0.93 0.93 AUTHOR ::::EMDATABANK.org::::EMD-39683:::: Cryo-EM structure of a tri-heme cytochrome-associated RC-LH1 complex from a marine photoheterotrophic bacterium, purified with magnesium-containing solutions-half-map-B