Photosystem II from Arabidopsis thaliana

2026-09-02 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES chem_comp_atom citation citation_author em_admin pdbx_validate_chiral _chem_comp_atom.pdbx_stereo_config _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY chem_comp chem_comp_atom chem_comp_bond em_admin pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order pdbx_struct_conn_angle pdbx_unobs_or_zero_occ_atoms pdbx_validate_close_contact struct_conn struct_conn_type _chem_comp.formula _chem_comp_atom.pdbx_stereo_config _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update PDBe PDBe 2025-01-26 2026-03-25 2026-03-25 2026-09-02 Sven och Lilly Lawskis fond for naturvetenskaplig forskning Sweden Swedish Research Council 2020-03809 Sweden Carl Trygger Foundation CTS 19.324 Sweden Kempe Foundation JCK-2030 Sweden German Research Foundation (DFG) TP A5 Germany Photosystem II from Arabidopsis thaliana Forsman JA Graca AT Hussein R Hall M Messinger J Schroder WP Aydin AO Membrane bound, Photosystem II, Arabidopsis, Manganese cluster, oxidoreductase, PHOTOSYNTHESIS Forsman J Graca AT Aydin AO Hall M Hussein R Schroder WP Messinger J The structure of intact and active Photosystem II from Arabidopsis thaliana at 2.44 angstrom resolution. New Phytol. UK 250 3014 3025 2026 41958335 doi:10.1111/nph.71085 1469-8137 9i4t FULLOVERLAP EMDB EMD-52620 associated EM volume

C2S2-type Photosystem II complex from Arabidopsis thaliana C2S2-type Photosystem II complex from Arabidopsis thaliana 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Arabidopsis thaliana Columbia-0 Leaves Thylakoid membranes 1.118 Photosystem II protein D1 Arabidopsis thaliana Columbia-0 Leaves 0.038961277 2 LEVO MTAILERRESESLWGRFCNWITSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVDIDGIREPVSGSLLYGNNIISG AIIPTSAAIGLHFYPIWEAASVDEWLYNGGPYELIVLHFLLGVACYMGREWELSFRLGMRPWIAVAYSAPVAAATAVFLI YPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESANEGYRFG QEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGIWFTALGISTMAFNLNGFNFNQSVVDSQGRVINTWADI INRANLGMEVMHERNAHNFPLDLAAVEAPSTNG P83755 1.10.3.9 Photosystem II CP47 reaction center protein Arabidopsis thaliana Columbia-0 Leaves 0.056091824 2 LEVO MGLPWYRVHTVVLNDPGRLLAVHIMHTALVAGWAGSMALYELAVFDPSDPVLDPMWRQGMFVIPFMTRLGITNSWGGWNI TGGTITNPGLWSYEGVAGAHIVFSGLCFLAAIWHWVYWDLEIFCDERTGKPSLDLPKIFGIHLFLSGVACFGFGAFHVTG LYGPGIWVSDPYGLTGKVQPVNPAWGVEGFDPFVPGGIASHHIAAGTLGILAGLFHLSVRPPQRLYKGLRMGNIETVLSS SIAAVFFAAFVVAGTMWYGSATTPIELFGPTRYQWDQGYFQQEIYRRVSAGLAENQSLSEAWAKIPEKLAFYDYIGNNPA KGGLFRAGSMDNGDGIAVGWLGHPVFRNKEGRELFVRRMPTFFETFPVVLVDGDGIVRADVPFRRAESKYSVEQVGVTVE FYGGELNGVSYSDPATVKKYARRAQLGEIFELDRATLKSDGVFRSSPRGWFTFGHASFALLFFFGHIWHGARTLFRDVFA GIDPDLDAQVEFGAFQKLGDPTTKRQAV P56777 Photosystem II CP43 reaction center protein Arabidopsis thaliana Columbia-0 Leaves 0.051915499999999996 2 LEVO MKTLYSLRRFYHVETLFNGTLALAGRDQETTGFAWWAGNARLINLSGKLLGAHVAHAGLIVFWAGAMNLFEVAHFVPEKP MYEQGLILLPHLATLGWGVGPGGEVIDTFPYFVSGVLHLISSAVLGFGGIYHALLGPETLEESFPFFGYVWKDRNKMTTI LGIHLILLGVGAFLLVFKALYFGGVYDTWAPGGGDVRKITNLTLSPSVIFGYLLKSPFGGEGWIVSVDDLEDIIGGHVWL GSICIFGGIWHILTKPFAWARRALVWSGEAYLSYSLAALSVCGFIACCFVWFNNTAYPSEFYGPTGPEASQAQAFTFLVR DQRLGANVGSAQGPTGLGKYLMRSPTGEVIFGGETMRFWDLRAPWLEPLRGPNGLDLSRLKKDIQPWQERRSAEYMTHAP LGSLNSVGGVATEINAVNYVSPRSWLSTSHFVLGFFLFVGHLWHAGRARAAAAGFEKGIDRDFEPVLSMTPLN P56778 Photosystem II D2 protein Arabidopsis thaliana Columbia-0 Leaves 0.039575281000000004 2 LEVO MTIALGKFTKDEKDLFDIMDDWLRRDRFVFVGWSGLLLFPCAYFALGGWFTGTTFVTSWYTHGLASSYLEGCNFLTAAVS TPANSLAHSLLLLWGPEAQGDFTRWCQLGGLWAFVALHGAFALIGFMLRQFELARSVQLRPYNAIAFSGPIAVFVSVFLI YPLGQSGWFFAPSFGVAAIFRFILFFQGFHNWTLNPFHMMGVAGVLGAALLCAIHGATVENTLFEDGDGANTFRAFNPTQ AEETYSMVTANRFWSQIFGVAFSNKRWLHFFMLFVPVTGLWMSALGVVGLALNLRAYDFVSQEIRAAEDPEFETFYTKNI LLNEGIRAWMAAQDQPHENLIFPEEVLPRGNAL P56761 1.10.3.9 Cytochrome b559 subunit alpha Arabidopsis thaliana Columbia-0 Leaves 0.009393501 2 LEVO MSGSTGERSFADIITSIRYWVIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNEYFTESRQGIPLITGRFDSLEQLDEFS RSF P56779 Cytochrome b559 subunit beta Arabidopsis thaliana Columbia-0 Leaves 0.004488323999999999 2 LEVO MTIDRTYPIFTVRWLAVHGLAVPTVFFLGSISAMQFIQR P62095 Chlorophyll a-b binding protein 1, chloroplastic Arabidopsis thaliana Columbia-0 Leaves 0.028266062 4 LEVO MAASTMALSSPAFAGKAVKLSPAASEVLGSGRVTMRKTVAKPKGPSGSPWYGSDRVKYLGPFSGESPSYLTGEFPGDYGW DTAGLSADPETFARNRELEVIHSRWAMLGALGCVFPELLARNGVKFGEAVWFKAGSQIFSDGGLDYLGNPSLVHAQSILA IWATQVILMGAVEGYRVAGNGPLGEAEDLLYPGGSFDPLGLATDPEAFAELKVKELKNGRLAMFSMFGFFVQAIVTGKGP IENLADHLADPVNNNAWAFATNFVPGK P04778 Photosystem II reaction center protein H Arabidopsis thaliana Columbia-0 Leaves 0.007706886999999999 2 LEVO MATQTVEDSSRSGPRSTTVGKLLKPLNSEYGKVAPGWGTTPLMGVAMALFAVFLSIILEIYNSSVLLDGISVN P56780 Photosystem II reaction center protein I Arabidopsis thaliana Columbia-0 Leaves 0.0041708909999999995 2 LEVO MLTLKLFVYTVVIFFVSLFIFGFLSNDPGRNPGREE P62100 Photosystem II reaction center protein J Arabidopsis thaliana Columbia-0 Leaves 0.004117832 2 LEVO MADTTGRIPLWVIGTVAGILVIGLIGIFFYGSYSGLGSSL P56781 Photosystem II reaction center protein K Arabidopsis thaliana Columbia-0 Leaves 0.006977381 2 LEVO MLNIFNLICIFFNSTLFSSTFLVAKLPEAYAFLNPIVDVMPVIPLFFLLLAFVWQAAVSFR P56782 Photosystem II reaction center protein L Arabidopsis thaliana Columbia-0 Leaves 0.004471075 2 LEVO MTQSNPNEQSVELNRTSLYWGLLLIFVLAVLFSNYFFN P60129 Photosystem II reaction center protein M Arabidopsis thaliana Columbia-0 Leaves 0.003783538 2 LEVO MEVNILAFIATALFILVPTAFLLIIYVKTVSQND P62109 Oxygen-evolving enhancer protein 1-1, chloroplastic Arabidopsis thaliana Columbia-0 Leaves 0.035180262000000004 2 LEVO MAASLQSTATFLQSAKIATAPSRGSSHLRSTQAVGKSFGLETSSARLTCSFQSDFKDFTGKCSDAVKIAGFALATSALVV SGASAEGAPKRLTYDEIQSKTYMEVKGTGTANQCPTIDGGSETFSFKPGKYAGKKFCFEPTSFTVKADSVSKNAPPEFQN TKLMTRLTYTLDEIEGPFEVASDGSVNFKEEDGIDYAAVTVQLPGGERVPFLFTVKQLDASGKPDSFTGKFLVPSYRGSS FLDPKGRGGSTGYDNAVALPAGGRGDEEELVKENVKNTAASVGEITLKVTKSKPETGEVIGVFESLQPSDTDLGAKVPKD VKIQGVWYGQLE P23321 Oxygen-evolving enhancer protein 2-1, chloroplastic Arabidopsis thaliana Columbia-0 Leaves 0.028125189 2 LEVO MAYSACFLHQSALASSAARSSSSSSSQRHVSLSKPVQIICKAQQSHEDDNSAVSRRLALTLLVGAAAVGSKVSPADAAYG EAANVFGKPKTNTDFLPYNGDGFKVQVPAKWNPSKEIEYPGQVLRFEDNFDATSNLNVMVTPTDKKSITDYGSPEEFLSQ VNYLLGKQAYFGETASEGGFDNNAVATANILESSSQEVGGKPYYYLSVLTRTADGDEGGKHQLITATVNGGKLYICKAQA GDKRWFKGARKFVESAATSFSVA Q42029 Oxygen-evolving enhancer protein 3-1, chloroplastic Arabidopsis thaliana Columbia-0 Leaves 0.023899219 2 LEVO MASMGGLHGASPAVLEGSLKINGSSRLNGSGRVAVAQRSRLVVRAQQSEETSRRSVIGLVAAGLAGGSFVQAVLADAISI KVGPPPAPSGGLPAGTDNSDQARDFALALKDRFYLQPLPPTEAAARAKESAKDIINVKPLIDRKAWPYVQNDLRSKASYL RYDLNTIISSKPKDEKKSLKDLTTKLFDTIDNLDYAAKKKSPSQAEKYYAETVSALNEVLAKLG Q9XFT3 Chlorophyll a-b binding protein CP29.1, chloroplastic Arabidopsis thaliana Columbia-0 Leaves 0.031170338 2 LEVO MAATSAAAAAASSIMGTRVAPGIHPGSGRFTAVFGFGKKKAAPKKSAKKTVTTDRPLWYPGAISPDWLDGSLVGDYGFDP FGLGKPAEYLQFDIDSLDQNLAKNLAGDVIGTRTEAADAKSTPFQPYSEVFGIQRFRECELIHGRWAMLATLGALSVEWL TGVTWQDAGKVELVDGSSYLGQPLPFSISTLIWIEVLVIGYIEFQRNAELDSEKRLYPGGKFFDPLGLAADPEKTAQLQL AEIKHARLAMVAFLGFAVQAAATGKGPLNNWATHLSDPLHTTIIDTFSSS Q07473 Chlorophyll a-b binding protein CP26, chloroplastic Arabidopsis thaliana Columbia-0 Leaves 0.030187576 2 LEVO MASLGVSEMLGTPLNFRAVSRSSAPLASSPSTFKTVALFSKKKPAPAKSKAVSETSDELAKWYGPDRRIFLPDGLLDRSE IPEYLNGEVAGDYGYDPFGLGKKPENFAKYQAFELIHARWAMLGAAGFIIPEALNKYGANCGPEAVWFKTGALLLDGNTL NYFGKNIPINLVLAVVAEVVLLGGAEYYRITNGLDFEDKLHPGGPFDPLGLAKDPEQGALLKVKEIKNGRLAMFAMLGFF IQAYVTGEGPVENLAKHLSDPFGNNLLTVIAGTAERAPTL Q9XF89 Photosystem II reaction center protein T Arabidopsis thaliana Columbia-0 Leaves 0.0038256419999999998 2 LEVO MEALVYTFLLVSTLGIIFFAIFFREPPKISTKK P61839 Photosystem II 5 kDa protein, chloroplastic Arabidopsis thaliana Columbia-0 Leaves 0.011042852 2 LEVO MASMTMTATFFPAVAKVPSATGGRRLSVVRASTSDNTPSLEVKEQSSTTMRRDLMFTAAAAAVCSLAKVAMAEEEEPKRG TEAAKKKYAQVCVTMPTAKICRY Q39195 Photosystem II reaction center W protein, chloroplastic Arabidopsis thaliana Columbia-0 Leaves 0.013685823 2 LEVO MASFTASASTVSAARPALLLKPTVAISAPVLGLPPMGKKKGGVRCSMETKQGNVSVMGAGVSAAATAALTAVMSNPAMAL VDERMSTEGTGLPFGLSNNLLGWILFGVFGLIWTFFFVYTSSLEEDEESGLSL Q39194 Expressed protein Arabidopsis thaliana Columbia-0 Leaves 0.011826013 2 LEVO MASTSAMSLVTPLNQTRSSPFLKPLPLKPSKALVATGGRAQRLQVKALKMDKALTGISAAALTASMVIPEIAEAAGSGIS PSLKNFLLSIASGGLVLTVIIGVVVGVSNFDPVKRT Q9SKI3 Chlorophyll a-b binding protein 2.1, chloroplastic Arabidopsis thaliana Columbia-0 Leaves 0.028673388999999997 2 LEVO MATSAIQQSSFAGQTALKPSNELLRKVGVSGGGRVTMRRTVKSTPQSIWYGPDRPKYLGPFSENTPSYLTGEYPGDYGWD TAGLSADPETFAKNRELEVIHSRWAMLGALGCTFPEILSKNGVKFGEAVWFKAGSQIFSEGGLDYLGNPNLIHAQSILAI WAVQVVLMGFIEGYRIGGGPLGEGLDPLYPGGAFDPLNLAEDPEAFSELKVKELKNGRLAMFSMFGFFVQAIVTGKGPIE NLFDHLADPVANNAWSYATNFVPGN Q9SHR7 Photosystem II reaction center protein Z Arabidopsis thaliana Columbia-0 Leaves 0.006569768 2 LEVO MTIAFQLAVFALIITSSILLISVPVVFASPDGWSSNKNVVFSGTSLWIGLVFLVGILNSLIS P56790 CHLORIDE ION 3.5453e-05 4 CL CHLOROPHYLL A 0.000893489 156 CLA PHEOPHYTIN A 0.0008712 4 PHO BETA-CAROTENE 0.000536873 22 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 FE (II) ION 5.5845e-05 2 FE2 BICARBONATE ION 6.1017e-05 2 BCT DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 10 DGD 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 10 LMG CA-MN4-O5 CLUSTER 0.00033982699999999996 2 OEX DODECYL-BETA-D-MALTOSIDE 0.000510615 2 LMT 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 18 LHG PROTOPORPHYRIN IX CONTAINING FE 0.000616487 2 HEM CHLOROPHYLL B 0.000907472 50 CHL (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL 0.000568871 18 LUT (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL 0.00060087 8 XAT (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL 0.00060087 10 NEX water 1.8015e-05 1206 HOH singleParticle particle 9.7 6.0 50.0 C6H13NO4S 2-(N-morpholino)ethanesulfonic acid 20.0 CaCl2 Calcium Chloride 5.0 MgCl2 Magnesium Chloride 0.6 C5H11NO2 Betaine 0.03 C24H46O11 n-Dodecyl-b-D-maltoside Quantifoil R1.2/1.3 COPPER 200 GLOW DISCHARGE 30

50 mA

ETHANE 100 277 FEI VITROBOT MARK IV

Thylakoid membranes were solubilised using b-dodecylmaltoside. The C2S2-type Photosystem II complexes were isolated using sucrose gradients.

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