Cryo-EM structure of apo-Photosystem II from Synechocystis sp. PCC 6803

2026-08-12 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY NON_POLYMER_DESCRIPTION chem_comp chem_comp_atom chem_comp_bond database_2 pdbx_validate_chiral _chem_comp.formula _database_2.pdbx_DOI _database_2.pdbx_database_accession REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY chem_comp_atom em_admin 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 struct_conn _chem_comp_atom.pdbx_stereo_config _em_admin.last_update _pdbx_entry_details.has_protein_modification EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update RCSB RCSB 2020-04-12 2020-08-26 2020-08-26 2026-08-12 Department of Energy (DOE, United States) DE-FG02-05ER15646 United States Cryo-EM structure of apo-Photosystem II from Synechocystis sp. PCC 6803 Gisriel CJ Photosystem, oxidoreductase, water-splitting, photoactivation, PHOTOSYNTHESIS Gisriel CJ Zhou K Huang H Debus RJ Xiong Y Brudvig GW Cryo-EM Structure of Monomeric Photosystem II from Synechocystis sp. PCC 6803 Lacking the Water-Oxidation Complex Joule US 2020 doi:10.1016/j.joule.2020.07.016 2542-4351 6wj6 FULLOVERLAP EMDB EMD-21690 associated EM volume

Cryo-EM structure of apo-photosystem II from Synechocystis sp. PCC 6803

apo-Photosystem II apo-Photosystem II 0 1 2 3 4 5 6 7 8 9 10 11 12 13 Synechocystis sp. (strain PCC 6803 / Kazusa) PCC 6803 / Kazusa 0.267067 Photosystem II protein D1 2 Synechocystis sp. (strain PCC 6803 / Kazusa) PCC 6803 / Kazusa 0.039744116999999995 1 LEVO MTTTLQQRESASLWEQFCQWVTSTNNRIYVGWFGTLMIPTLLTATTCFIIAFIAAPPVDIDGIREPVAGSLLYGNNIISG AVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLVVFHFLIGIFCYMGRQWELSYRLGMRPWICVAYSAPVSAATAVFLI YPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLVRETTEVESQNYGYKFG QEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLGAWPVIGIWFTAMGVSTMAFNLNGFNFNQSILDSQGRVIGTWADV LNRANIGFEVMHERNAHNFPLDLASGEQAPVALTAPAVNG P16033 1.10.3.9 Photosystem II CP47 reaction center protein Synechocystis sp. (strain PCC 6803 / Kazusa) PCC 6803 / Kazusa 0.055954355 1 LEVO MGLPWYRVHTVVLNDPGRLISVHLMHTALVAGWAGSMALYELAIFDSSDAVLNPMWRQGMFVLPFMARLGVTSSWNGWSV TGETGLDPGFWSFEGVAAAHIVLSGLLFLAAVWHWVFWDLELFVDPRTGESALDLPKMFGIHLFLSGLLCFGFGAFHLTG VWGPGMWVSDPYGLTGHVQPVAPEWGPAGFNPFNPGGVVAHHIAAGIVGIIAGLFHLTVRPPERLYKALRMGNIETVLSS SIAAVFFAAFVVAGTMWYGNATTPIELFGPTRYQWDKGYFQEEIQRRVDSQLAEGASLSEAWSTIPEKLAFYDYVGNSPA KGGLFRTGAMNSGDGIAQEWIGHPIFKDKEGRELEVRRMPNFFETFPVIMTDADGVVRADIPFRRSESKFSVEQTGVTVS FYGGALDGQTFSNPSDVKKFARKAQLGEGFDFDTETFNSDGVFRTSPRGWFTFGHAVFALLFFFGHIWHGSRTLFRDVFA GVDPGLEEQVEFGVFAKVGDLSTRKEA P05429 Photosystem II CP43 reaction center protein Synechocystis sp. (strain PCC 6803 / Kazusa) PCC 6803 / Kazusa 0.050330694999999995 1 LEVO MVTLSNTSMVGGRDLPSSGFAWWSGNARLINLSGKLLGAHVAHAGLIVFWAGAMTLFEVAHFIPEKPMYEQGLILLPHIA TLGWGVGPAGEVTDIFPFFVVGVLHLISSAVLGLGGIYHALRGPEVLEEYSSFFGYDWKDKNQMTNIIGYHLILLGCGAL LLVFKAMFFGGVYDTWAPGGGDVRVITNPTLNPAIIFGYLLKAPFGGEGWIISVNNMEDIIGGHIWIGLICISGGIWHIL TKPFGWARRALIWSGEAYLSYSLGALSLMGFIASVFVWFNNTAYPSEFYGPTGMEASQSQAFTFLVRDQRLGANIASAQG PTGLGKYLMRSPSGEIIFGGETMRFWDFRGPWLEPLRGPNGLDLDKLRNDIQPWQVRRAAEYMTHAPLGSLNSVGGVITD VNSFNYVSPRAWLATSHFVLGFFFLVGHLWHAGRARAAAAGFEKGIDRETEPTLFMPDLD P09193 Photosystem II D2 protein Synechocystis sp. (strain PCC 6803 / Kazusa) PCC 6803 / Kazusa 0.039519238 1 LEVO MTIAVGRAPVERGWFDVLDDWLKRDRFVFIGWSGLLLFPCAFMALGGWLTGTTFVTSWYTHGLASSYLEGANFLTVAVSS PADAFGHSLLFLWGPEAQGNLTRWFQIGGLWPFVALHGAFGLIGFMLRQFEISRLVGIRPYNAIAFSGPIAVFVSVFLMY PLGQSSWFFAPSFGVAGIFRFILFLQGFHNWTLNPFHMMGVAGILGGALLCAIHGATVENTLFEDGEDSNTFRAFEPTQA EETYSMVTANRFWSQIFGIAFSNKRWLHFFMLFVPVTGLWMSSVGIVGLALNLRAYDFVSQELRAAEDPEFETFYTKNIL LNEGMRAWMAPQDQPHENFIFPEEVLPRGNAL P09192 1.10.3.9 Cytochrome b559 subunit alpha Synechocystis sp. (strain PCC 6803 / Kazusa) PCC 6803 / Kazusa 0.009454576999999999 1 LEVO MSGTTGERPFSDIVTSIRYWVIHSITIPMLFIAGWLFVSTGLAYDAFGTPRPDEYFTQTRQELPILQERYDINQEIQEFN Q P09190 Cytochrome b559 subunit beta Synechocystis sp. (strain PCC 6803 / Kazusa) PCC 6803 / Kazusa 0.0049357839999999995 1 LEVO MATQNPNQPVTYPIFTVRWLAVHTLAVPSVFFVGAIAAMQFIQR P09191 Photosystem II reaction center protein H Synechocystis sp. (strain PCC 6803 / Kazusa) PCC 6803 / Kazusa 0.007120404 1 LEVO MAQRTRLGDILRPLNSEYGKVVPGWGTTPVMGVFMALFLVFLLIILQIYNSSLILEGFSVDWAG P14835 Photosystem II reaction center protein I Synechocystis sp. (strain PCC 6803 / Kazusa) PCC 6803 / Kazusa 0.004310109 1 LEVO MLTLKIAVYIVVGLFISLFIFGFLSSDPTRNPGRKDFE Q54697 Photosystem II reaction center protein K Synechocystis sp. (strain PCC 6803 / Kazusa) PCC 6803 / Kazusa 0.005114127 1 LEVO METIYLLAKLPEAYQIFDPLVDVLPVIPLFFLALAFVWQAAVGFK P15819 Photosystem II reaction center protein L Synechocystis sp. (strain PCC 6803 / Kazusa) PCC 6803 / Kazusa 0.004476145 1 LEVO MDRNSNPNRQPVELNRTSLYLGLLLVAVLGILFSSYFFN Q55354 Photosystem II reaction center protein M Synechocystis sp. (strain PCC 6803 / Kazusa) PCC 6803 / Kazusa 0.0038826299999999998 1 LEVO MQVNNLGFIASILFVLVPTVFLLILFIQTGKQSES P72701 Photosystem II reaction center protein T Synechocystis sp. (strain PCC 6803 / Kazusa) PCC 6803 / Kazusa 0.003543308 1 LEVO MESVAYILVLTMALAVLFFAIAFREPPRIEK P74787 Photosystem II reaction center X protein Synechocystis sp. (strain PCC 6803 / Kazusa) PCC 6803 / Kazusa 0.004189036 1 LEVO MTPSLANFLWSLVLGAAIVLIPATVGLIFISQKDKITRS P72575 FE (II) ION 5.5845e-05 1 FE2 CHLOROPHYLL A 0.000893489 35 CLA PHEOPHYTIN A 0.0008712 2 PHO BETA-CAROTENE 0.000536873 9 BCR 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL 0.0007951159999999999 7 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 2 PL9 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 3 LMG DODECYL-BETA-D-MALTOSIDE 0.000510615 2 LMT DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 2 DGD CHLORIDE ION 3.5453e-05 1 CL BICARBONATE ION 6.1017e-05 1 BCT 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 4 LHG PROTOPORPHYRIN IX CONTAINING FE 0.000616487 1 HEM N-FORMYLMETHIONINE 0.000177221 3 FME water 1.8015e-05 198 HOH singleParticle particle 0.025 7.0

10 mM HEPES pH 7.0 100 mM NaCl 0.03% beta-dodecylmaltoside

C-flat-2/1 COPPER 300 CARBON HOLEY GLOW DISCHARGE 30 ETHANE 100 298 FEI VITROBOT MARK IV

Monodisperse single particles

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) 48.07 1 NONE

Homology

C1 2.58 FSC 0.143 CUT-OFF RELION 3.1 212640 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_21690.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 302.4 302.4 302.4 90.0 90.0 90.0 X Y Z -0.11423279 0.24345654 -0.00007884522 0.0075905714 1.18125 1.18125 1.18125 0.0394 AUTHOR ::::EMDATABANK.org::::EMD-21690:::: apo-photosystem II