Cryo-EM Structure of PSII at 1.95 angstrom resolution

2026-08-12 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY REFINEMENT_DESCRIPTION database_2 em_3d_fitting_list em_admin pdbx_initial_refinement_model _database_2.pdbx_DOI _database_2.pdbx_database_accession _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 chem_comp chem_comp_atom chem_comp_bond database_2 em_3d_fitting_list em_admin pdbx_entry_details pdbx_initial_refinement_model pdbx_modification_feature pdbx_validate_chiral struct_conn _chem_comp.formula _database_2.pdbx_DOI _database_2.pdbx_database_accession _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 _pdbx_entry_details.has_protein_modification _struct_conn.pdbx_leaving_atom_flag DERIVED_CALCULATIONS atom_site chem_comp_atom chem_comp_bond em_admin pdbx_struct_conn_angle struct_conf 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.label_atom_id _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 EXPERIMENTAL_SUMMARY em_admin _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 2020-09-15 2021-03-31 2021-03-31 2026-08-12 Cryo-EM Structure of PSII at 1.95 angstrom resolution Kato K Miyazaki N Photosystem II, PHOTOSYNTHESIS Kato K Miyazaki N Hamaguchi T Nakajima Y Akita F Yonekura K Shen JR High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams. Commun Biol UK 4 382 382 2021 33753866 doi:10.1038/s42003-021-01919-3 2399-3642 7d1t FULLOVERLAP EMDB EMD-30547 associated EM volume

PSII dimer PSII dimer 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 Thermosynechococcus vulcanus 0.725 Photosystem II protein D1 Thermosynechococcus vulcanus 0.037029233999999994 2 LEVO ANLWERFCNWVTSTDNRLYVGWFGVIMIPTLLAATICFVIAFIAAPPVDIDGIREPVSGSLLYGNNIITGAVVPSSNAIG LHFYPIWEAASLDEWLYNGGPYQLIIFHFLLGASCYMGRQWELSYRLGMRPWICVAYSAPLASAFAVFLIYPIGQGSFSD GMPLGISGTFNFMIVFQAEHNILMHPFHQLGVAGVFGGALFCAMHGSLVTSSLIRETTETESANYGYKFGQEEETYNIVA AHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGVWFAALGISTMAFNLNGFNFNHSVIDAKGNVINTWADIINRANLGMEV MHERNAHNFPLDLA P51765 1.10.3.9 Photosystem II CP47 reaction center protein Thermosynechococcus vulcanus 0.056068742 2 LEVO GLPWYRVHTVLINDPGRLIAAHLMHTALVAGWAGSMALYELATFDPSDPVLNPMWRQGMFVLPFMARLGVTGSWSGWSIT GETGIDPGFWSFEGVALAHIVLSGLLFLAACWHWVYWDLELFRDPRTGEPALDLPKMFGIHLFLAGLLCFGFGAFHLTGL FGPGMWVSDPYGLTGSVQPVAPEWGPDGFNPYNPGGVVAHHIAAGIVGIIAGLFHILVRPPQRLYKALRMGNIETVLSSS IAAVFFAAFVVAGTMWYGSATTPIELFGPTRYQWDSSYFQQEINRRVQASLASGATLEEAWSAIPEKLAFYDYIGNNPAK GGLFRTGPMNKGDGIAQAWKGHAVFRNKEGEELFVRRMPAFFESFPVILTDKNGVVKADIPFRRAESKYSFEQQGVTVSF YGGELNGQTFTDPPTVKSYARKAIFGEIFEFDTETLNSDGIFRTSPRGWFTFAHAVFALLFFFGHIWHGARTLFRDVFSG IDPELSPEQVEWGFYQKVGDVTTRK D0VWR1 Photosystem II CP43 reaction center protein Thermosynechococcus vulcanus 0.04920725 2 LEVO ATNRDQESSGFAWWAGNARLINLSGKLLGAHVAHAGLIVFWAGAMTLFELAHFIPEKPMYEQGLILIPHIATLGWGVGPG GEVVDTFPFFVVGVVHLISSAVLGFGGVYHAIRGPETLEEYSSFFGYDWKDKNKMTTILGFHLIVLGIGALLLVAKAMFF GGLYDTWAPGGGDVRVITNPTLDPRVIFGYLLKSPFGGEGWIVSVNNLEDVVGGHIWIGLICIAGGIWHILTTPFGWARR AFIWSGEAYLSYSLGALSMMGFIATCFVWFNNTVYPSEFYGPTGPEASQAQAMTFLIRDQKLGANVGSAQGPTGLGKYLM RSPTGEIIFGGETMRFWDFRGPWLEPLRGPNGLDLNKIKNDIQPWQERRAAEYMTHAPLGSLNSVGGVATEINSVNFVSP RSWLATSHFVLAFFFLVGHLWHAGRARAAAAGFEKGIDRESEPVLSMPSLD D0VWR7 Photosystem II D2 protein Thermosynechococcus vulcanus 0.038419941 2 LEVO ERGWFDILDDWLKRDRFVFVGWSGILLFPCAYLALGGWLTGTTFVTSWYTHGLASSYLEGCNFLTVAVSTPANSMGHSLL LLWGPEAQGDFTRWCQLGGLWTFIALHGAFGLIGFMLRQFEIARLVGVRPYNAIAFSAPIAVFVSVFLIYPLGQSSWFFA PSFGVAAIFRFLLFFQGFHNWTLNPFHMMGVAGVLGGALLCAIHGATVENTLFQDGEGASTFRAFNPTQAEETYSMVTAN RFWSQIFGIAFSNKRWLHFFMLFVPVTGLWMSAIGVVGLALNLRSYDFISQEIRAAEDPEFETFYTKNLLLNEGIRAWMA PQDQP(HSK)ENFVFPEEVLPRGNAL D0VWR8 1.10.3.9 Cytochrome b559 subunit alpha Thermosynechococcus vulcanus 0.009321514999999999 2 LEVO TTGERPFSDIITSVRYWVIHSITIPALFIAGWLFVSTGLAYDVFGTPRPDSYYAQEQRSIPLVTDRFEAKQQVETFLEQL K P12238 Cytochrome b559 subunit beta Thermosynechococcus vulcanus 0.0038686109999999997 2 LEVO SYPIFTVRWVAVHTLAVPTIFFLGAIAAMQFIQR P12239 Photosystem II reaction center protein H Thermosynechococcus vulcanus 0.007057349 2 LEVO ARRTWLGDILRPLNSEYGKVAPGWGTTPLMAVFMGLFLVFLLIILEIYNSTLILDGVNVSWKA P19052 Photosystem II reaction center protein I Thermosynechococcus vulcanus 0.004195983 2 LEVO (FME)ETLKITVYIVVTFFVLLFVFGFLSGDPARNPKRKD P12240 Photosystem II reaction center protein J Thermosynechococcus vulcanus 0.003756439 2 LEVO EGGRIPLWIVATVAGMGVIVIVGLFFYGAYAGLGSSL Q7DGD4 Photosystem II reaction center protein K Thermosynechococcus vulcanus 0.004101911 2 LEVO KLPEAYAIFDPLVDVLPVIPVLFLALAFVWQAAVGFR P19054 Photosystem II reaction center protein L Thermosynechococcus vulcanus 0.004299043999999999 2 LEVO MEPNPNRQPVELNRTSLYLGLLLILVLALLFSSYFFN P12241 Photosystem II reaction center protein M Thermosynechococcus vulcanus 0.003835527 2 LEVO (FME)EVNQLGLIATALFVLVPSVFLIILYVQTESQQK P12312 Photosystem II manganese-stabilizing polypeptide Thermosynechococcus vulcanus 0.026651706999999997 2 LEVO QTLTYDDIVGTGLANKCPTLDDTARGAYPIDSSQTYRIARLCLQPTTFLVKEEPKNKRQEAEFVPTKLVTRETTSLDQIQ GELKVNSDGSLTFVEEDGIDFQPVTVQMAGGERIPLLFTVKNLVASTQPNVTSITTSTDFKGEFNVPSYRTANFLDPKGR GLASGYDSAIALPQAKEEELARANVKRFSLTKGQISLNVAKVDGRTGEIAGTFESEQLSDDDMGAHEPHEVKIQGVFYAS IEPA D0VWR2 Photosystem II reaction center protein T Thermosynechococcus vulcanus 0.003777559 2 LEVO (FME)ETITYVFIFACIIALFFFAIFFREPPRITK P12313 Photosystem II 12 kDa extrinsic protein Thermosynechococcus vulcanus 0.010966316999999998 2 LEVO ELVNVVDEKLGTAYGEKIDLNNTNIAAFIQYRGLYPTLAKLIVKNAPYESVEDVLNIPGLTERQKQILRENLEHFTVTEV ETALVEGGDRYNNGLYK P56152 Cytochrome c-550 Thermosynechococcus vulcanus 0.015148255 2 LEVO AELTPEVLTVPLNSEGKTITLTEKQYLEGKRLFQYACASCHVGGITKTNPSLDLRTETLALATPPRDNIEGLVDYMKNPT TYDGEQEIAEVHPSLRSADIFPKMRNLTEKDLVAIAGHILVEPKILGDKWGGGKVYY P0A387 Photosystem II reaction center protein Ycf12 Thermosynechococcus vulcanus 0.0032280349999999998 2 LEVO EVIAQLTMIAMIGIAGPMIIFLLAVRRGNL D0VWR3 Photosystem II reaction center protein X Thermosynechococcus vulcanus 0.004191029999999999 2 LEVO TITPSLKGFFIGLLSGAVVLGLTFAVLIAISQIDKVQRSL D0VWR4 Photosystem II reaction center protein Z Thermosynechococcus vulcanus 0.006766187 2 LEVO MTILFQLALAALVILSFVMVIGVPVAYASPQDWDRSKQLIFLGSGLWIALVLVVGVLNFFVV D0VWR5 Photosystem II protein Y Thermosynechococcus vulcanus 0.003859732 2 LEVO DWRVLVVLLPVLLAAGWAVRNILPYAVKQVQKLL P0DM37 CA-MN4-O5 CLUSTER 0.00033982699999999996 2 OEX FE (II) ION 5.5845e-05 2 FE2 CHLORIDE ION 3.5453e-05 4 CL CHLOROPHYLL A 0.000893489 70 CLA PHEOPHYTIN A 0.0008712 4 PHO BETA-CAROTENE 0.000536873 20 BCR 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL 0.0007951159999999999 8 SQD 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 4 PL9 UNKNOWN LIGAND 36 UNL 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 10 LMG DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 8 DGD DODECYL-BETA-D-MALTOSIDE 0.000510615 8 LMT BICARBONATE ION 6.1017e-05 2 BCT 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 10 LHG PROTOPORPHYRIN IX CONTAINING FE 0.000616487 2 HEM MAGNESIUM ION 2.4305e-05 2 MG HEME C 0.0006205189999999999 2 HEC (3R)-beta,beta-caroten-3-ol 0.0005528719999999999 2 RRX water 1.8015e-05 2432 HOH singleParticle particle 2.0 6.0 20.0 MES-NaOH 0.04 DDM Quantifoil R1.2/1.3 COPPER 200 CARBON PLASMA CLEANING 30 ETHANE 100 277 FEI VITROBOT MARK IV JEOL CRYO ARM 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) COUNTING 83.0 1 CTFFIND 4.1 PHASE FLIPPING AND AMPLITUDE CORRECTION 3WU2 C2 FOURIER SPACE 1.95 FSC 0.143 CUT-OFF RELION 3.0 174099 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_30547.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 328.80002 328.80002 328.80002 90.0 90.0 90.0 X Y Z -0.097950734 0.24216053 0.00016159083 0.0045615123 0.822 0.822 0.822 0.025 AUTHOR ::::EMDATABANK.org::::EMD-30547:::: 3WU2 PDB experimental model FLEXIBLE FIT REAL emd_30547_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 328.80002 328.80002 328.80002 90.0 90.0 90.0 X Y Z -0.032406025 0.097416446 0.00027372234 0.0035074335 0.822 0.822 0.822 AUTHOR ::::EMDATABANK.org::::EMD-30547:::: emd_30547_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 328.80002 328.80002 328.80002 90.0 90.0 90.0 X Y Z -0.031932615 0.09826239 0.00027359862 0.003501115 0.822 0.822 0.822 AUTHOR ::::EMDATABANK.org::::EMD-30547::::