Coordinates of Cryo-EM structure of the Arabidopsis thaliana C2S2M2-type PSII supercomplex

2025-10-08 REL PDBc INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBj PDBc 2025-01-07 2025-10-08 2025-10-08 2025-10-08 National Natural Science Foundation of China (NSFC) China Coordinates of Cryo-EM structure of the Arabidopsis thaliana C2S2M2-type PSII supercomplex Chen SJB Wu C Wu JH Sui SF Zhang LX photosystem, PLANT PROTEIN, PHOTOSYNTHESIS Chen SJB Wu C Wu JH Sui SF Zhang LX Coordinates of Cryo-EM structure of the Arabidopsis thaliana C2S2M2-type PSII supercomplex To Be Published 0353 EMD-63017 consensus EM volume EMD-66068 focused EM volume EMD-66069 focused EM volume EMD-66070 focused EM volume 9le8 FULLOVERLAP EMDB EMD-63017 consensus EM volume EMDB EMD-63018 associated EM volume

EMDB EMD-66068 focused EM volume EMDB EMD-66069 focused EM volume EMDB EMD-66070 focused EM volume Cryo-EM structure of the Arabidopsis thaliana photosystem II(PSII-LHCII-ST2) Cryo-EM structure of the Arabidopsis thaliana photosystem II(PSII-LHCII-ST2) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 Arabidopsis thaliana Chlorophyll a-b binding protein, chloroplastic Arabidopsis thaliana 0.028193934 4 LEVO MAASTMALSSPALTGKAVKLSPAASEVFGTGRITMRKASKPTGPSGSPWYGSDRVKYLGPFSGEPPSYLTGEFPGDYGWD TAGLSADPETFARNRELEVIHSRWAMLGALGCVFPELLARNGVKFGEAVWFKAGSQIFSDGGLDYLGNPSLVHAQSILAI WATQVILMGAVEGYRVAGDGPLGEAEDLLYPGGSFDPLGLATDPEAFAELKVKELKNGRLAMFSMFGFFVQAIVTGKGPL ENLADHLADPVNNNAWAFATNFVPGK A0A654EYS2 Chlorophyll a-b binding protein 3, chloroplastic Arabidopsis thaliana 0.02645299 2 LEVO ASSFNPLRDVVSLGSPKYTMGNDLWYGPDRVKYLGPFSVQTPSYLTGEFPGDYGWDTAGLSADPEAFAKNRALEVIHGRW AMLGAFGCITPEVLQKWVRVDFKEPVWFKAGSQIFSEGGLDYLGNPNLVHAQSILAVLGFQVILMGLVEGFRINGLDGVG EGNDLYPGGQYFDPLGLADDPVTFAELKVKEIKNGRLAMFSMFGFFVQAIVTGKGPLENLLDHLDNPVANNAWAFATKFA PGA Q9S7M0 Chlorophyll a-b binding protein, chloroplastic Arabidopsis thaliana 0.023198286999999998 2 LEVO AAAAAQPKKSWIPAVKGGGNFLDPEWLDGSLPGDFGFDPLGLGKDPAFLKWYREAELIHGRWAMAAVLGIFVGQAWSGVA WFEAGAQPDAIAPFSFGSLLGTQLLLMGWVESKRWVDFFNPDSQSVEWATPWSKTAENFANYTGDQGYPGGRFFDPLGLA GKNRDGVYEPDFEKLERLKLAEIKHSRLAMVAMLIFYFEAGQGKTPLGALGL A0A178WK60 Photosystem II protein D1 Arabidopsis thaliana 0.038830082 2 LEVO TAILERRESESLWGRFCNWITSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVDIDGIREPVSGSLLYGNNIISGA IIPTSAAIGLHFYPIWEAASVDEWLYNGGPYELIVLHFLLGVACYMGREWELSFRLGMRPWIAVAYSAPVAAATAVFLIY PIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESANEGYRFGQ EEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGIWFTALGISTMAFNLNGFNFNQSVVDSQGRVINTWADII NRANLGMEVMHERNAHNFPLDLAAVEAPSTNG P83755 1.10.3.9 Photosystem II CP47 reaction center protein Arabidopsis thaliana 0.056091824 2 LEVO MGLPWYRVHTVVLNDPGRLLAVHIMHTALVAGWAGSMALYELAVFDPSDPVLDPMWRQGMFVIPFMTRLGITNSWGGWNI TGGTITNPGLWSYEGVAGAHIVFSGLCFLAAIWHWVYWDLEIFCDERTGKPSLDLPKIFGIHLFLSGVACFGFGAFHVTG LYGPGIWVSDPYGLTGKVQPVNPAWGVEGFDPFVPGGIASHHIAAGTLGILAGLFHLSVRPPQRLYKGLRMGNIETVLSS SIAAVFFAAFVVAGTMWYGSATTPIELFGPTRYQWDQGYFQQEIYRRVSAGLAENQSLSEAWAKIPEKLAFYDYIGNNPA KGGLFRAGSMDNGDGIAVGWLGHPVFRNKEGRELFVRRMPTFFETFPVVLVDGDGIVRADVPFRRAESKYSVEQVGVTVE FYGGELNGVSYSDPATVKKYARRAQLGEIFELDRATLKSDGVFRSSPRGWFTFGHASFALLFFFGHIWHGARTLFRDVFA GIDPDLDAQVEFGAFQKLGDPTTKRQAV P56777 Photosystem II CP43 reaction center protein Arabidopsis thaliana 0.050086324 2 LEVO TLFNGTLALAGRDQETTGFAWWAGNARLINLSGKLLGAHVAHAGLIVFWAGAMNLFEVAHFVPEKPMYEQGLILLPHLAT LGWGVGPGGEVIDTFPYFVSGVLHLISSAVLGFGGIYHALLGPETLEESFPFFGYVWKDRNKMTTILGIHLILLGVGAFL LVFKALYFGGVYDTWAPGGGDVRKITNLTLSPSVIFGYLLKSPFGGEGWIVSVDDLEDIIGGHVWLGSICIFGGIWHILT KPFAWARRALVWSGEAYLSYSLAALSVCGFIACCFVWFNNTAYPSEFYGPTGPEASQAQAFTFLVRDQRLGANVGSAQGP TGLGKYLMRSPTGEVIFGGETMRFWDLRAPWLEPLRGPNGLDLSRLKKDIQPWQERRSAEYMTHAPLGSLNSVGGVATEI NAVNYVSPRSWLSTSHFVLGFFLFVGHLWHAGRARAAAAGFEKGIDRDFEPVLSMTPLN P56778 Photosystem II D2 protein Arabidopsis thaliana 0.039444082 2 LEVO TIALGKFTKDEKDLFDIMDDWLRRDRFVFVGWSGLLLFPCAYFALGGWFTGTTFVTSWYTHGLASSYLEGCNFLTAAVST PANSLAHSLLLLWGPEAQGDFTRWCQLGGLWAFVALHGAFALIGFMLRQFELARSVQLRPYNAIAFSGPIAVFVSVFLIY PLGQSGWFFAPSFGVAAIFRFILFFQGFHNWTLNPFHMMGVAGVLGAALLCAIHGATVENTLFEDGDGANTFRAFNPTQA EETYSMVTANRFWSQIFGVAFSNKRWLHFFMLFVPVTGLWMSALGVVGLALNLRAYDFVSQEIRAAEDPEFETFYTKNIL LNEGIRAWMAAQDQPHENLIFPEEVLPRGNAL P56761 1.10.3.9 Cytochrome b559 subunit alpha Arabidopsis thaliana 0.009393501 2 LEVO MSGSTGERSFADIITSIRYWVIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNEYFTESRQGIPLITGRFDSLEQLDEFS RSF P56779 Cytochrome b559 subunit beta Arabidopsis thaliana 0.004428228 2 LEVO MTIDRTYPIFTVRWLAVHGLAVPTVSFLGSISAMQFIQR P62095 Chlorophyll a-b binding protein 1, chloroplastic Arabidopsis thaliana 0.024885071999999998 6 LEVO RKTVAKPKGPSGSPWYGSDRVKYLGPFSGESPSYLTGEFPGDYGWDTAGLSADPETFARNRELEVIHSRWAMLGALGCVF PELLARNGVKFGEAVWFKAGSQIFSDGGLDYLGNPSLVHAQSILAIWATQVILMGAVEGYRVAGNGPLGEAEDLLYPGGS FDPLGLATDPEAFAELKVKELKNGRLAMFSMFGFFVQAIVTGKGPIENLADHLADPVNNNAWAFATNFVPGK P04778 Photosystem II reaction center protein H Arabidopsis thaliana 0.007575691 2 LEVO ATQTVEDSSRSGPRSTTVGKLLKPLNSEYGKVAPGWGTTPLMGVAMALFAVFLSIILEIYNSSVLLDGISVN P56780 Photosystem II reaction center protein I Arabidopsis thaliana 0.0041708909999999995 2 LEVO MLTLKLFVYTVVIFFVSLFIFGFLSNDPGRNPGREE P62100 Photosystem II reaction center protein K Arabidopsis thaliana 0.004239112 2 LEVO KLPEAYAFLNPIVDVMPVIPLFFLLLAFVWQAAVSFR P56782 Photosystem II reaction center protein L Arabidopsis thaliana 0.004471075 2 LEVO MTQSNPNEQSVELNRTSLYWGLLLIFVLAVLFSNYFFN P60129 Photosystem II reaction center protein M Arabidopsis thaliana 0.003783538 2 LEVO MEVNILAFIATALFILVPTAFLLIIYVKTVSQND P62109 Chlorophyll a-b binding protein CP29.1, chloroplastic Arabidopsis thaliana 0.027302854999999997 2 LEVO AAPKKSAKKTVTTDRPLWYPGAISPDWLDGSLVGDYGFDPFGLGKPAEYLQFDIDSLDQNLAKNLAGDVIGTRTEAADAK STPFQPYSEVFGIQRFRECELIHGRWAMLATLGALSVEWLTGVTWQDAGKVELVDGSSYLGQPLPFSISTLIWIEVLVIG YIEFQRNAELDSEKRLYPGGKFFDPLGLAADPEKTAQLQLAEIKHARLAMVAFLGFAVQAAATGKGPLNNWATHLSDPLH TTIIDTFSSS Q07473 Chlorophyll a-b binding protein CP26, chloroplastic Arabidopsis thaliana 0.025232754 2 LEVO SKAVSETSDELAKWYGPDRRIFLPDGLLDRSEIPEYLNGEVAGDYGYDPFGLGKKPENFAKYQAFELIHARWAMLGAAGF IIPEALNKYGANCGPEAVWFKTGALLLDGNTLNYFGKNIPINLVLAVVAEVVLLGGAEYYRITNGLDFEDKLHPGGPFDP LGLAKDPEQGALLKVKEIKNGRLAMFAMLGFFIQAYVTGEGPVENLAKHLSDPFGNNLLTVIAGTAERAPTL Q9XF89 Photosystem II reaction center protein T Arabidopsis thaliana 0.0038256419999999998 2 LEVO MEALVYTFLLVSTLGIIFFAIFFREPPKISTKK P61839 Photosystem II 5 kDa protein, chloroplastic Arabidopsis thaliana 0.00317881 2 LEVO EPKRGTEAAKKKYAQVCVTMPTAKICRY Q39195 Photosystem II reaction center W protein, chloroplastic Arabidopsis thaliana 0.006036748999999999 2 LEVO LVDERMSTEGTGLPFGLSNNLLGWILFGVFGLIWTFFFVYTSSLEEDEESGLSL Q39194 (thale cress) hypothetical protein Arabidopsis thaliana 0.004186916 2 LEVO AGSGISPSLKNFLLSIASGGLVLTVIIGVVVGVSNFDPVKRT A0A7G2E9B1 Photosystem II reaction center protein Z Arabidopsis thaliana 0.006569768 2 LEVO MTIAFQLAVFALIITSSILLISVPVVFASPDGWSSNKNVVFSGTSLWIGLVFLVGILNSLIS P56790 CHLOROPHYLL B 0.000907472 95 CHL CHLOROPHYLL A 0.000893489 215 CLA (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL 0.000568871 31 LUT (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 11 NEX (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 5 XAT 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 22 LHG BETA-CAROTENE 0.000536873 24 BCR CA-MN4-O5 CLUSTER 0.00033982699999999996 2 OEX FE (II) ION 5.5845e-05 2 FE2 PHEOPHYTIN A 0.0008712 4 PHO 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 10 LMG 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL 0.0007951159999999999 8 SQD DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 9 DGD BICARBONATE ION 6.1017e-05 2 BCT 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 PROTOPORPHYRIN IX CONTAINING FE 0.000616487 2 HEM singleParticle particle 7.4 ETHANE FEI TALOS ARCTICA OTHER OTHER FIELD EMISSION GUN 300 1.2 2.2 GATAN K3 (6k x 4k) 50.5 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 3.37 FSC 0.143 CUT-OFF cryoSPARC 38544 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_63018.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 583.2 583.2 583.2 90.0 90.0 90.0 Z Y X -23.600860000000001 57.685886000000004 0.02746084 1.3427253 1.35 1.35 1.35 4.62 AUTHOR 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