Structure of monomeric photosystem II

2026-08-12 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY database_2 em_admin _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update DERIVED_CALCULATIONS atom_site chem_comp_atom chem_comp_bond em_admin pdbx_struct_conn_angle struct_conf struct_conn _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_atom_id _atom_site.label_alt_id _atom_site.label_atom_id _atom_site.occupancy _atom_site.type_symbol _chem_comp_atom.atom_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _em_admin.last_update 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 _chem_comp.formula _chem_comp.formula_weight _em_admin.last_update _entity.formula_weight STRUCTURE_SUMMARY em_admin entity _em_admin.last_update _entity.formula_weight PDBj PDBj 2021-03-15 2021-07-07 2021-07-07 2026-08-12 Japan Society for the Promotion of Science (JSPS) JP19K22396 Japan Japan Society for the Promotion of Science (JSPS) JP20H03194 Japan Japan Society for the Promotion of Science (JSPS) JP20H02914 Japan Japan Society for the Promotion of Science (JSPS) JP17H06434 Japan Japan Science and Technology JPMJPR16P1 Japan Japan Agency for Medical Research and Development (AMED) JP18am0101072 Japan Structure of monomeric photosystem II Yu H Hamaguchi T Photosynthesis, Photosystem, membrane protein Yu H Hamaguchi T Nakajima Y Kato K Kawakami K Akita F Yonekura K Shen JR Cryo-EM structure of monomeric photosystem II at 2.78 angstrom resolution reveals factors important for the formation of dimer. Biochim Biophys Acta Bioenerg NE 1862 148471 148471 2021 34216574 doi:10.1016/j.bbabio.2021.148471 1879-2650 7eda FULLOVERLAP EMDB EMD-31062 associated EM volume

Photosystem II Photosystem II 0 1 2 3 4 5 6 8 9 10 11 12 13 14 15 16 17 18 19 20 Thermosynechococcus vulcanus Photosystem II protein D1 Thermosynechococcus vulcanus 0.037029233999999994 1 LEVO ANLWERFCNWVTSTDNRLYVGWFGVIMIPTLLAATICFVIAFIAAPPVDIDGIREPVSGSLLYGNNIITGAVVPSSNAIG LHFYPIWEAASLDEWLYNGGPYQLIIFHFLLGASCYMGRQWELSYRLGMRPWICVAYSAPLASAFAVFLIYPIGQGSFSD GMPLGISGTFNFMIVFQAEHNILMHPFHQLGVAGVFGGALFCAMHGSLVTSSLIRETTETESANYGYKFGQEEETYNIVA AHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGVWFAALGISTMAFNLNGFNFNHSVIDAKGNVINTWADIINRANLGMEV MHERNAHNFPLDLA P51765 1.10.3.9 Photosystem II CP47 reaction center protein Thermosynechococcus vulcanus 0.055939562 1 LEVO GLPWYRVHTVLINDPGRLIAAHLMHTALVAGWAGSMALYELATFDPSDPVLNPMWRQGMFVLPFMARLGVTGSWSGWSIT GETGIDPGFWSFEGVALAHIVLSGLLFLAACWHWVYWDLELFRDPRTGEPALDLPKMFGIHLFLAGLLCFGFGAFHLTGL FGPGMWVSDPYGLTGSVQPVAPEWGPDGFNPYNPGGVVAHHIAAGIVGIIAGLFHILVRPPQRLYKALRMGNIETVLSSS IAAVFFAAFVVAGTMWYGSATTPIELFGPTRYQWDSSYFQQEINRRVQASLASGATLEEAWSAIPEKLAFYDYIGNNPAK GGLFRTGPMNKGDGIAQAWKGHAVFRNKEGEELFVRRMPAFFESFPVILTDKNGVVKADIPFRRAESKYSFEQQGVTVSF YGGELNGQTFTDPPTVKSYARKAIFGEIFEFDTETLNSDGIFRTSPRGWFTFAHAVFALLFFFGHIWHGARTLFRDVFSG IDPELSPEQVEWGFYQKVGDVTTR D0VWR1 Photosystem II CP43 reaction center protein Thermosynechococcus vulcanus 0.04920725 1 LEVO ATNRDQESSGFAWWAGNARLINLSGKLLGAHVAHAGLIVFWAGAMTLFELAHFIPEKPMYEQGLILIPHIATLGWGVGPG GEVVDTFPFFVVGVVHLISSAVLGFGGVYHAIRGPETLEEYSSFFGYDWKDKNKMTTILGFHLIVLGIGALLLVAKAMFF GGLYDTWAPGGGDVRVITNPTLDPRVIFGYLLKSPFGGEGWIVSVNNLEDVVGGHIWIGLICIAGGIWHILTTPFGWARR AFIWSGEAYLSYSLGALSMMGFIATCFVWFNNTVYPSEFYGPTGPEASQAQAMTFLIRDQKLGANVGSAQGPTGLGKYLM RSPTGEIIFGGETMRFWDFRGPWLEPLRGPNGLDLNKIKNDIQPWQERRAAEYMTHAPLGSLNSVGGVATEINSVNFVSP RSWLATSHFVLAFFFLVGHLWHAGRARAAAAGFEKGIDRESEPVLSMPSLD D0VWR7 Photosystem II D2 protein Thermosynechococcus vulcanus 0.038290828 1 LEVO RGWFDILDDWLKRDRFVFVGWSGILLFPCAYLALGGWLTGTTFVTSWYTHGLASSYLEGCNFLTVAVSTPANSMGHSLLL LWGPEAQGDFTRWCQLGGLWTFIALHGAFGLIGFMLRQFEIARLVGVRPYNAIAFSAPIAVFVSVFLIYPLGQSSWFFAP SFGVAAIFRFLLFFQGFHNWTLNPFHMMGVAGVLGGALLCAIHGATVENTLFQDGEGASTFRAFNPTQAEETYSMVTANR FWSQIFGIAFSNKRWLHFFMLFVPVTGLWMSAIGVVGLALNLRSYDFISQEIRAAEDPEFETFYTKNLLLNEGIRAWMAP QDQP(HSK)ENFVFPEEVLPRGNAL D0VWR8 1.10.3.9 Cytochrome b559 subunit alpha Thermosynechococcus vulcanus 0.00958084 1 LEVO MAGTTGERPFSDIITSVRYWVIHSITIPALFIAGWLFVSTGLAYDVFGTPRPDSYYAQEQRSIPLVTDRFEAKQQVETFL EQLK P12238 Cytochrome b559 subunit beta Thermosynechococcus vulcanus 0.005067899999999999 1 LEVO MTSNTPNQEPVSYPIFTVRWVAVHTLAVPTIFFLGAIAAMQFIQR P12239 Photosystem II reaction center protein H Thermosynechococcus vulcanus 0.006986271 1 LEVO ARRTWLGDILRPLNSEYGKVAPGWGTTPLMAVFMGLFLVFLLIILEIYNSTLILDGVNVSWK P19052 Photosystem II reaction center protein I Thermosynechococcus vulcanus 0.004438255 1 LEVO (FME)ETLKITVYIVVTFFVLLFVFGFLSGDPARNPKRKDLE P12240 Photosystem II reaction center protein J Thermosynechococcus vulcanus 0.004105908 1 LEVO MMSEGGRIPLWIVATVAGMGVIVIVGLFFYGAYAGLGSSL Q7DGD4 Photosystem II reaction center protein K Thermosynechococcus vulcanus 0.004101911 1 LEVO KLPEAYAIFDPLVDVLPVIPVLFLALAFVWQAAVGFR P19054 Photosystem II reaction center protein L Thermosynechococcus vulcanus 0.004299043999999999 1 LEVO MEPNPNRQPVELNRTSLYLGLLLILVLALLFSSYFFN P12241 Photosystem II reaction center protein M Thermosynechococcus vulcanus 0.0032898989999999998 1 LEVO VNQLGLIATALFVLVPSVFLIILYVQTESQ P12312 Photosystem II manganese-stabilizing polypeptide Thermosynechococcus vulcanus 0.026651706999999997 1 LEVO QTLTYDDIVGTGLANKCPTLDDTARGAYPIDSSQTYRIARLCLQPTTFLVKEEPKNKRQEAEFVPTKLVTRETTSLDQIQ GELKVNSDGSLTFVEEDGIDFQPVTVQMAGGERIPLLFTVKNLVASTQPNVTSITTSTDFKGEFNVPSYRTANFLDPKGR GLASGYDSAIALPQAKEEELARANVKRFSLTKGQISLNVAKVDGRTGEIAGTFESEQLSDDDMGAHEPHEVKIQGVFYAS IEPA D0VWR2 Photosystem II reaction center protein T Thermosynechococcus vulcanus 0.0036483789999999998 1 LEVO (FME)ETITYVFIFACIIALFFFAIFFREPPRIT P12313 Photosystem II 12 kDa extrinsic protein Thermosynechococcus vulcanus 0.011655986 1 LEVO ATASTEEELVNVVDEKLGTAYGEKIDLNNTNIAAFIQYRGLYPTLAKLIVKNAPYESVEDVLNIPGLTERQKQILRENLE HFTVTEVETALVEGGDRYNNGLYK P56152 Cytochrome c-550 Thermosynechococcus vulcanus 0.018046943 1 LEVO MLKKCVWLAVALCLCLWQFTMGTALAAELTPEVLTVPLNSEGKTITLTEKQYLEGKRLFQYACASCHVGGITKTNPSLDL RTETLALATPPRDNIEGLVDYMKNPTTYDGEQEIAEVHPSLRSADIFPKMRNLTEKDLVAIAGHILVEPKILGDKWGGGK VYY P0A387 Photosystem II reaction center protein Ycf12 Thermosynechococcus vulcanus 0.0032280349999999998 1 LEVO EVIAQLTMIAMIGIAGPMIIFLLAVRRGNL D0VWR3 Photosystem II reaction center protein X Thermosynechococcus vulcanus 0.004191029999999999 1 LEVO TITPSLKGFFIGLLSGAVVLGLTFAVLIAISQIDKVQRSL D0VWR4 Photosystem II reaction center protein Z Thermosynechococcus vulcanus 0.006766187 1 LEVO MTILFQLALAALVILSFVMVIGVPVAYASPQDWDRSKQLIFLGSGLWIALVLVVGVLNFFVV D0VWR5 Photosystem II protein Y Thermosynechococcus vulcanus 0.003859732 1 LEVO DWRVLVVLLPVLLAAGWAVRNILPYAVKQVQKLL P0DM37 CA-MN4-O5 CLUSTER 0.00033982699999999996 1 OEX FE (II) ION 5.5845e-05 1 FE2 CHLOROPHYLL A 0.000893489 35 CLA PHEOPHYTIN A 0.0008712 2 PHO BETA-CAROTENE 0.000536873 8 BCR 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL 0.0007951159999999999 2 SQD 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 3 LMG 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE 0.000749201 2 PL9 UNKNOWN LIGAND 0.0009492989999999999 1 UNL DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 4 DGD BICARBONATE ION 6.1017e-05 1 BCT 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 4 LHG PROTOPORPHYRIN IX CONTAINING FE 0.000616487 1 HEM (3R)-beta,beta-caroten-3-ol 0.0005528719999999999 1 RRX HEME C 0.0006205189999999999 1 HEC water 1.8015e-05 16 HOH singleParticle particle 6.0 ETHANE JEOL CRYO ARM 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K3 (6k x 4k) 70.0 1 NONE 2.78 FSC 0.143 CUT-OFF 173875 NOT APPLICABLE NOT APPLICABLE 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