Semi-active PSII dimer from native Peak4 PSII dimers

2026-08-12 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond em_admin pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_struct_conn_angle pdbx_validate_chiral struct_conn _chem_comp_atom.pdbx_stereo_config _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update PDBe PDBe 2024-07-18 2025-07-30 2025-07-30 2026-08-12 Biotechnology and Biological Sciences Research Council (BBSRC) BB/I00937X/1 United Kingdom Biotechnology and Biological Sciences Research Council (BBSRC) BB/V002007/1 United Kingdom Semi-active PSII dimer from native Peak4 PSII dimers Zhao Z Vercellino I Nixon PJ Sazanov LA PSII, native intermediate, photodamage, PSII assembly, PHOTOSYNTHESIS Zhao Z Vercellino I Nixon PJ Sazanov LA Semi-active PSII dimer from the Peak4 PSII dimers To Be Published 0353 9g6g FULLOVERLAP EMDB EMD-51101 associated EM volume

PDB 9G6F unspecified

inactive PSII dimer from the native Peak4 PSII

PDB 9G6H unspecified

active PSII dimer from the native Peak4 PSII

Semi-active PSII dimer with one PSII lacking extrinsic subunits Semi-active PSII dimer with one PSII lacking extrinsic subunits 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

This semi-active complex is a PSII dimer with one monomer containing the extrinsic subunits, while the other monomer lacks the extrinsic subunits. This structure was obtained from the Peak4 PSII, which was eluted as the fourth fraction in the ion exchange chromatography after the nickel affinity pull-down.

Thermosynechococcus vestitus BP-1 thylakoid membrane Photosystem II protein D1 1 Thermosynechococcus vestitus BP-1 0.039762309 1 LEVO MTTTLQRRESANLWERFCNWVTSTDNRLYVGWFGVIMIPTLLAATICFVIAFIAAPPVDIDGIREPVSGSLLYGNNIITG AVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLIIFHFLLGASCYMGRQWELSYRLGMRPWICVAYSAPLASAFAVFLI YPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHQLGVAGVFGGALFCAMHGSLVTSSLIRETTETESANYGYKFG QEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGVWFTALGISTMAFNLNGFNFNHSVIDAKGNVINTWADI INRANLGMEVMHERNAHNFPLDLASAESAPVAMIAPSING P0A444 1.10.3.9 Photosystem II CP47 reaction center protein Thermosynechococcus vestitus BP-1 0.056656457 2 LEVO MGLPWYRVHTVLINDPGRLIAAHLMHTALVAGWAGSMALYELATFDPSDPVLNPMWRQGMFVLPFMARLGVTGSWSGWSI TGETGIDPGFWSFEGVALAHIVLSGLLFLAACWHWVYWDLELFRDPRTGEPALDLPKMFGIHLFLAGLLCFGFGAFHLTG LFGPGMWVSDPYGLTGSVQPVAPEWGPDGFNPYNPGGVVAHHIAAGIVGIIAGLFHILVRPPQRLYKALRMGNIETVLSS SIAAVFFAAFVVAGTMWYGSATTPIELFGPTRYQWDSSYFQQEINRRVQASLASGATLEEAWSAIPEKLAFYDYIGNNPA KGGLFRTGPMNKGDGIAQAWKGHAVFRNKEGEELFVRRMPAFFESFPVILTDKNGVVKADIPFRRAESKYSFEQQGVTVS FYGGELNGQTFTDPPTVKSYARKAIFGEIFEFDTETLNSDGIFRTSPRGWFTFAHAVFALLFFFGHIWHGARTLFRDVFS GIDPELSPEQVEWGFYQKVGDVTTRRKEAV Q8DIQ1 Photosystem II CP43 reaction center protein Thermosynechococcus vestitus BP-1 0.0502875 2 LEVO MVTLSSNSIFATNRDQESSGFAWWAGNARLINLSGKLLGAHVAHAGLIVFWAGAMTLFELAHFIPEKPMYEQGLILIPHI ATLGWGVGPGGEVVDTFPFFVVGVVHLISSAVLGFGGVYHAIRGPETLEEYSSFFGYDWKDKNKMTTILGFHLIVLGIGA LLLVAKAMFFGGLYDTWAPGGGDVRVITNPTLDPRVIFGYLLKSPFGGEGWIVSVNNLEDVVGGHIWIGLICIAGGIWHI LTTPFGWARRAFIWSGEAYLSYSLGALSMMGFIATCFVWFNNTVYPSEFYGPTGPEASQAQAMTFLIRDQKLGANVGSAQ GPTGLGKYLMRSPTGEIIFGGETMRFWDFRGPWLEPLRGPNGLDLNKIKNDIQPWQERRAAEYMTHAPLGSLNSVGGVAT EINSVNFVSPRSWLATSHFVLAFFFLVGHLWHAGRARAAAAGFEKGIDRESEPVLSMPSLD Q8DIF8 Photosystem II D2 protein Thermosynechococcus vestitus BP-1 0.039388156 2 LEVO MTIAIGRAPAERGWFDILDDWLKRDRFVFVGWSGILLFPCAYLALGGWLTGTTFVTSWYTHGLASSYLEGCNFLTVAVST PANSMGHSLLLLWGPEAQGDFTRWCQLGGLWTFIALHGAFGLIGFMLRQFEIARLVGVRPYNAIAFSAPIAVFVSVFLIY PLGQSSWFFAPSFGVAAIFRFLLFFQGFHNWTLNPFHMMGVAGVLGGALLCAIHGATVENTLFQDGEGASTFRAFNPTQA EETYSMVTANRFWSQIFGIAFSNKRWLHFFMLFVPVTGLWMSAIGVVGLALNLRSYDFISQEIRAAEDPEFETFYTKNLL LNEGIRAWMAPQDQPHENFVFPEEVLPRGNAL Q8CM25 1.10.3.9 Cytochrome b559 subunit alpha Thermosynechococcus vestitus BP-1 0.00958084 2 LEVO MAGTTGERPFSDIITSVRYWVIHSITIPALFIAGWLFVSTGLAYDVFGTPRPDSYYAQEQRSIPLVTDRFEAKQQVETFL EQLK Q8DIP0 Cytochrome b559 subunit beta Thermosynechococcus vestitus BP-1 0.005067899999999999 2 LEVO MTSNTPNQEPVSYPIFTVRWVAVHTLAVPTIFFLGAIAAMQFIQR Q8DIN9 Photosystem II reaction center protein H Thermosynechococcus vestitus BP-1 0.0073587539999999995 2 LEVO MARRTWLGDILRPLNSEYGKVAPGWGTTPLMAVFMGLFLVFLLIILEIYNSTLILDGVNVSWKALG Q8DJ43 Photosystem II reaction center protein I Thermosynechococcus vestitus BP-1 0.004438255 2 LEVO (FME)ETLKITVYIVVTFFVLLFVFGFLSGDPARNPKRKDLE Q8DJZ6 Photosystem II reaction center protein J Thermosynechococcus vestitus BP-1 0.004105908 2 LEVO MMSEGGRIPLWIVATVAGMGVIVIVGLFFYGAYAGLGSSL P59087 Photosystem II reaction center protein K Thermosynechococcus vestitus BP-1 0.005028082999999999 2 LEVO MIDALVLVAKLPEAYAIFDPLVDVLPVIPVLFLALAFVWQAAVGFR Q9F1K9 Photosystem II reaction center protein L Thermosynechococcus vestitus BP-1 0.004299043999999999 2 LEVO MEPNPNRQPVELNRTSLYLGLLLILVLALLFSSYFFN Q8DIN8 Photosystem II reaction center protein M Thermosynechococcus vestitus BP-1 0.003981673 2 LEVO MEVNQLGLIATALFVLVPSVFLIILYVQTESQQKSS Q8DHA7 Photosystem II manganese-stabilizing polypeptide Thermosynechococcus vestitus BP-1 0.029637443 1 LEVO MKYRILMATLLAVCLGIFSLSAPAFAAKQTLTYDDIVGTGLANKCPTLDDTARGAYPIDSSQTYRIARLCLQPTTFLVKE EPKNKRQEAEFVPTKLVTRETTSLDQIQGELKVNSDGSLTFVEEDGIDFQPVTVQMAGGERIPLLFTVKNLVASTQPNVT SITTSTDFKGEFNVPSYRTANFLDPKGRGLASGYDSAIALPQAKEEELARANVKRFSLTKGQISLNVAKVDGRTGEIAGT FESEQLSDDDMGAHEPHEVKIQGVFYASIEPA P0A431 Photosystem II reaction center protein T Thermosynechococcus vestitus BP-1 0.003906738 2 LEVO (FME)ETITYVFIFACIIALFFFAIFFREPPRITKK Q8DIQ0 Photosystem II 12 kDa extrinsic protein Thermosynechococcus vestitus BP-1 0.015030986 1 LEVO MQRLGRWLALAYFVGVSLLGWINWSAPTLAATASTEEELVNVVDEKLGTAYGEKIDLNNTNIAAFIQYRGLYPTLAKLIV KNAPYESVEDVLNIPGLTERQKQILRENLEHFTVTEVETALVEGGDRYNNGLYK Q9F1L5 Cytochrome c-550 Thermosynechococcus vestitus BP-1 0.018046943 1 LEVO MLKKCVWLAVALCLCLWQFTMGTALAAELTPEVLTVPLNSEGKTITLTEKQYLEGKRLFQYACASCHVGGITKTNPSLDL RTETLALATPPRDNIEGLVDYMKNPTTYDGEQEIAEVHPSLRSADIFPKMRNLTEKDLVAIAGHILVEPKILGDKWGGGK VYY P0A386 Photosystem II reaction center X protein Thermosynechococcus vestitus BP-1 0.004322225999999999 2 LEVO MTITPSLKGFFIGLLSGAVVLGLTFAVLIAISQIDKVQRSL Q9F1R6 Photosystem II reaction center protein Ycf12 Thermosynechococcus vestitus BP-1 0.005039142999999999 2 LEVO MGIFNGIIEFLSNINFEVIAQLTMIAMIGIAGPMIIFLLAVRRGNL Q8DJI1 Photosystem II reaction center protein Z Thermosynechococcus vestitus BP-1 0.006766187 2 LEVO MTILFQLALAALVILSFVMVIGVPVAYASPQDWDRSKQLIFLGSGLWIALVLVVGVLNFFVV Q8DHJ2 Photosystem II protein D1 1 Thermosynechococcus vestitus BP-1 0.039777301 1 LEVO MTTTLQRRESANLWERFCNWVTSTDNRLYVGWFGVIMIPTLLAATICFVIAFIAAPPVDIDGIREPVSGSLLYGNNIITG AVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLIIFHFLLGASCYMGRQWELSYRLGMRPWICVAYSAPLASAFAVFLI YPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHQLGVAGVFGGALFCAMHGSLVTSSLIRETTETESANYGYKFG QEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGVWFTALGISTMAFNLNGFNFNHSVIDAKGNVINTWADI INRANLGMEVM(HSK)ERNAHNFPLDLASAESAPVAMIAPSING P0A444 1.10.3.9 FE (II) ION 5.5845e-05 2 FE2 CHLORIDE ION 3.5453e-05 3 CL CHLOROPHYLL A 0.000893489 70 CLA PHEOPHYTIN A 0.0008712 4 PHO BETA-CAROTENE 0.000536873 20 BCR 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 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL 0.0007951159999999999 9 SQD EICOSANE 0.000282547 30 LFA CA-MN4-O5 CLUSTER 0.00033982699999999996 1 OEX DODECYL-BETA-D-MALTOSIDE 0.000510615 17 LMT BICARBONATE ION 6.1017e-05 2 BCT PALMITIC ACID 0.00025642399999999994 29 PLM 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 10 LMG GLYCEROL 9.209399999999999e-05 1 GOL DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 10 DGD 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 10 LHG PROTOPORPHYRIN IX CONTAINING FE 0.000616487 3 HEM (3R)-beta,beta-caroten-3-ol 0.0005528719999999999 2 RRX CALCIUM ION 4.0078e-05 1 CA water 1.8015e-05 960 HOH singleParticle particle 0.3 6.5

20 mM MES pH 6.5, 2.5 mM MgCl2, 2.5 mM CaCl2, 7 mM MgSO4, 0.03% DDM, 0.05% CHAPS

Quantifoil R0.6/1 COPPER 300 CARBON HOLEY GLOW DISCHARGE 5

The grids were glow-discharged for 5 sec at 25 mA before freezing.

ETHANE 100 277.15 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.6 2.0 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 BIOQUANTUM (6k x 4k) 1 9173 80.0 1 5900000 RELION 4.0.0 PHASE FLIPPING AND AMPLITUDE CORRECTION 7NHO

also with 3KZI

2.2 FSC 0.143 CUT-OFF 272215 MAXIMUM LIKELIHOOD RELION 4.0.0 MAXIMUM LIKELIHOOD RELION 4.0.0 RELION 4.0.0 emd_51101.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 238 417 274 324 213 287 274 417 238 137.0 208.5 119.0 90.0 90.0 90.0 Z Y X -0.12877771 0.38329488 0.003504643 0.025210757 0.5 0.5 0.5 0.039 AUTHOR ::::EMDATABANK.org::::EMD-51101:::: 7NHO a PDB experimental model 7NHO b PDB experimental model 7NHO c PDB experimental model 7NHO d PDB experimental model 7NHO e PDB experimental model 7NHO f PDB experimental model 7NHO h PDB experimental model 7NHO i PDB experimental model 3KZI j PDB experimental model 7NHO k PDB experimental model 7NHO l PDB experimental model 7NHO m PDB experimental model 7NHO t PDB experimental model 7NHO x PDB experimental model 7NHO y PDB experimental model 7NHO z PDB experimental model 3KZI A PDB experimental model 3KZI B PDB experimental model 3KZI C PDB experimental model 3KZI D PDB experimental model 3KZI E PDB experimental model 3KZI F PDB experimental model 3KZI H PDB experimental model 3KZI I PDB experimental model 3KZI J PDB experimental model 3KZI K PDB experimental model 3KZI L PDB experimental model 3KZI M PDB experimental model 3KZI T PDB experimental model 3KZI X PDB experimental model 3KZI Y PDB experimental model 3KZI Z PDB experimental model 3KZI O PDB experimental model 3KZI U PDB experimental model 3KZI V PDB experimental model FLEXIBLE FIT REAL emd_51101_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 424.4 424.4 424.4 90.0 90.0 90.0 X Y Z -0.055495597 0.16854657 -0.0000114484255 0.0055202963 1.061 1.061 1.061 AUTHOR ::::EMDATABANK.org::::EMD-51101:::: emd_51101_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 424.4 424.4 424.4 90.0 90.0 90.0 X Y Z -0.05374616 0.17536421 -0.000010789924 0.005518391 1.061 1.061 1.061 AUTHOR ::::EMDATABANK.org::::EMD-51101::::