In situ structure of the C2S2M2L4-type PSII-LHCII supercomplex from Oryza sativa

2026-10-07 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBj PDBj 2026-01-01 2026-10-07 2026-10-07 2026-10-07 National Natural Science Foundation of China (NSFC) 32201038 China In situ structure of the C2S2M2L4-type PSII-LHCII supercomplex from Oryza sativa Li J Elias E Zhang K Croce R Zhu J Photosystem II, C2S2M2L4-type, in situ, Oryza sativa, Chloroplast, Photosynthesis Li J Elias E Zhang K Croce R Zhu J In situ structures of plant photosystem supercomplexes. Nature UK 657 1094 1103 2026 42527593 doi:10.1038/s41586-026-10847-3 1476-4687 0006 NATUAS EMD-82229 consensus EM volume

In situ C2S2M2L4 supercomplex (consensus)

EMD-66946 focused EM volume

PSII-LHCII core (protomer 1)

EMD-66947 focused EM volume

PSII-LHCII core (protomer 2)

EMD-66951 focused EM volume

M-LHCII trimer with CP29/CP24 (protomer 1)

EMD-66952 focused EM volume

M-LHCII trimer with CP29/CP24 (protomer 2)

EMD-66949 focused EM volume

S-LHCII trimer with CP26 (protomer 1)

EMD-66950 focused EM volume

S-LHCII trimer with CP26 (protomer 2)

EMD-66971 focused EM volume

L-LHCII trimers (one side, protomer 1)

EMD-66974 focused EM volume

L-LHCII trimers (one side, protomer 2)

21wv FULLOVERLAP EMDB EMD-68060 associated EM volume

In situ structure of the C2S2M2L4-type PSII-LHCII supercomplex from Oryza sativa

EMDB EMD-82229 consensus EM volume

In situ C2S2M2L4 supercomplex (consensus)

EMDB EMD-66946 focused EM volume

PSII-LHCII core (protomer 1)

EMDB EMD-66947 focused EM volume

PSII-LHCII core (protomer 2)

EMDB EMD-66951 focused EM volume

M-LHCII trimer with CP29/CP24 (protomer 1)

EMDB EMD-66952 focused EM volume

M-LHCII trimer with CP29/CP24 (protomer 2)

EMDB EMD-66949 focused EM volume

S-LHCII trimer with CP26 (protomer 1)

EMDB EMD-66950 focused EM volume

S-LHCII trimer with CP26 (protomer 2)

EMDB EMD-66971 focused EM volume

L-LHCII trimers (one side, protomer 1)

EMDB EMD-66974 focused EM volume

L-LHCII trimers (one side, protomer 2)

Chloroplast Chloroplast 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 25 26 27 28 Oryza sativa Japonica Group Chlorophyll a-b binding protein 2, chloroplastic Oryza sativa Japonica Group 0.023441460999999997 14 LEVO GSPWYGADRVLYLGPLSGEPPSYLTGEFPGDYGWDTAGLSADPETFAKNRELEVIHSRWAMLGALGCVFPELLARNGVKF GEAVWFKAGSQIFSEGGLDYLGNPSLIHAQSILAIWAVQVVLMGAVEGYRIAGGPLGEVVDPLYPGGSFDPLGLADDPEA FAELKVKEIKNGRLAMFSMFGFFVQAIVTGKGPLENLADHLADPVNNNAWAYATNFVPG P12331 Chlorophyll a/b-binding protein Oryza sativa Japonica Group 0.024065338 2 LEVO ELWYGPDRVKYLGPFSAQTPSYLRGEFPGDYGWDTAGLSADPEAFARNRALEVIHGRWAMLGALGCITPEVLEKWVRVDF KEPVWFKAGAQIFSDGGLDYLGNPNLVHAQSILAVLGFQVVLMGLVEGYRINGLPGVGDGNDLYPGGQYFDPLGLADDPV TFAELKVKEIKNGRLAMFSMFGFFVQAIVTGKGPLENLLDHLADPVANNAWVYATKFTPG B7E6H8 Chlorophyll a-b binding protein, chloroplastic Oryza sativa Japonica Group 0.02255058 2 LEVO AKKSWIPAFKSDAEFINPPWLDGSLPGDFGFDPLGLGKDPAFLKWYREAELIHGRWAMAAVLGIFVGQAWSGVPWFEAGA QPEAIAPFSFGSLLGTQLLLMGWVESKRWVDFFNPDSQAVEWATPWSRTAENFSNATGEQGYPGGKFFDPLGLGGETRDG VYIPDTDKLDRLKLAEIKHARLAMLAMLIFYFEAGQGKTPLGALG Q7XV11 Chlorophyll a-b binding protein, chloroplastic Oryza sativa Japonica Group 0.02404515 4 LEVO APQSIWYGPDRPKYLGPFSEQTPSYLTGEFPGDYGWDTAGLSADPETFARNRELEVIHSRWAMLGALGCVFPEILSKNGV KFGEAVWFKAGAQIFSEGGLDYLGNPNLVHAQSILAIWAVQVVLMGFVEGYRVGGGPLGEGLDKVYPGGAFDPLGLADDP DTFAELKVKELKNGRLAMFSMFGFFVQAIVTGKGPIENLFDHVADPVANNAWAYATNFVPGK Q10HD0 Chlorophyll a-b binding protein 1, chloroplastic Oryza sativa Japonica Group 0.023368407999999997 4 LEVO SPWYGADRVLYLGPLSGEPPSYLTGEFPGDYGWDTAGLSADPETFAKNRELEVIHSRWAMLGALGCVFPELLARNGVKFG EAVWFKAGSQIFSEGGLDYLGNPSLIHAQSILAIWAVQVVLMGAVEGYRIAGGPLGEVVDPLYPGGAFDPLGLADDPEAF AELKVKEIKNGRLAMFSMFGFFVQAIVTGKGPLENLADHLADPVNNNAWAYATNFVPG P12330 Photosystem II protein D1 Oryza sativa Japonica Group 0.036917039 2 LEVO TSLWGRFCNWITSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVDIDGIREPVSGSLLYGNNIISGAIIPTSAAIG LHFYPIWEAASVDEWLYNGGPYELIVLHFLLGVACYMGREWELSFRLGMRPWIAVAYSAPVAAATAVFLIYPIGQGSFSD GMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESANEGYRFGQEEETYNIVA AHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGIWFTALGISTMAFNLNGFNFNQSVVDSQGRVINTWADIINRANLGMEV MHERNAHNFPLDLA P0C432 1.10.3.9 Photosystem II CP47 reaction center protein Oryza sativa Japonica Group 0.055632101999999996 2 LEVO GLPWYRVHTVVLNDPGRLLSVHIMHTALVSGWAGSMALYELAVFDPSDPVLDPMWRQGMFVIPFMTRLGITNSWGGWSIS GGTVTNPGIWSYEGVAGAHIVFSGLCFLAAIWHWVYWDLEIFCDERTGKPSLDLPKIFGIHLFLAGVACFGFGAFHVTGL YGPGIWVSDPYGLTGKVQAVNPAWGAEGFDPFVPGGIASHHIAAGTLGILAGLFHLSVRPPQRLYKGLRMGNIETVLSSS IAAVFFAAFVVAGTMWYGSATTPIELFGPTRYQWDQGYFQQEIYRRVSDGLAENLSLSEAWSKIPEKLAFYDYIGNNPAK GGLFRAGSMDNGDGIAVGWLGHPIFRDKEGRELFVRRMPTFFETFPVVLVDEEGIVRADVPFRRAESKYSVEQVGVTVEF YGGELNGVSYSDPATVKKYARRSQLGEIFELDRATLKSDGVFRSSPRGWFTFGHATFALLFFFGHIWHGARTLFRDVFAG IDPDLDAQVEFGTFQKVGDPTTR P0C362 Photosystem II CP43 reaction center protein Oryza sativa Japonica Group 0.049289438 2 LEVO AGRDQETTGFAWWAGNARLINLSGKLLGAHVAHAGLIVFWAGAMNLFEVAHFVPEKPMYEQGLILLPHLATLGWGVGPGG EVLDTFPYFVSGVLHLISSAVLGFGGIYHALLGPETLEESFPFFGYVWKDRNKMTTILGIHLILLGIGAFLLVLKALYFG GIYDTWAPGGGDVRKITNLTLSPGVIFGYLLKSPFGGEGWIVSVDDLEDIIGGHVWLGFICVFGGIWHILTKPFAWARRA FVWSGEAYLSYSLGALSVFGFIACCFVWFNNTAYPSEFYGPTGPEASQAQAFTFLVRDQRLGANVGSAQGPTGLGKYLMR SPTGEVIFGGETMRFWDLRAPWLEPLRGPNGLDLSRLKKDIQPWQERRSAEYMTHAPLGSLNSVGGVATEINAVNYVSPR SWLATSHFVLGFFFFVGHLWHAGRARAAAAGFEKGIDRDLEPVLYMTPLN P0C365 Photosystem II D2 protein Oryza sativa Japonica Group 0.038268645 2 LEVO NDLFDIMDDWLRRDRFVFVGWSGLLLFPCAYFALGGWFTGTTFVTSWYTHGLASSYLEGCNFLTAAVSTPANSLAHSLLL LWGPEAQGDFTRWCQLGGLWTFVALHGAFALIGFMLRQFELARSVQLRPYNAISFSGPIAVFVSVFLIYPLGQSGWFFAP SFGVAAIFRFILFFQGFHNWTLNPFHMMGVAGVLGAALLCAIHGATVENTLFEDGDGANTFRAFNPTQAEETYSMVTANR FWSQIFGVAFSNKRWLHFFMLFVPVTGLWMSAIGVVGLALNLRAYDFVSQEIRAAEDPEFETFYTKNILLNEGIRAWMAA QDQPHENLIFPEEVLPRGNAL P0C435 1.10.3.9 Cytochrome b559 subunit alpha Oryza sativa Japonica Group 0.00865469 2 LEVO RSFADIITSIRYWVIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNEYFTESRQGIPLITDRFDSLEQLDEFSRS P0C368 Cytochrome b559 subunit beta Oryza sativa Japonica Group 0.0040277789999999996 2 LEVO RTYPIFTVRWLAVHGLAVPTVFFLGSISAMQFIQR P0C401 Photosystem II reaction center protein H Oryza sativa Japonica Group 0.006472637999999999 2 LEVO GPRQTRVGNLLKPLNSEYGKVAPGWGTTPFMGVAMALFAVFLSIILEIYNSSVLLDGILM P0C420 Photosystem II reaction center protein I Oryza sativa Japonica Group 0.003912664 2 LEVO MLTLKLFVYTVVIFFVSLFIFGFLSNDPGRNPGR P0C405 Photosystem II reaction center protein J Oryza sativa Japonica Group 0.00358621 2 LEVO GRIPLWLIGTVTGIAVIGLIGVFFYGSYSGLGSSL P0C414 Photosystem II reaction center protein K Oryza sativa Japonica Group 0.004273127999999999 2 LEVO KLPEAYAIFNPIVDFMPVIPVLFFLLAFVWQAAVSFR P0C408 Photosystem II reaction center protein L Oryza sativa Japonica Group 0.0042658 2 LEVO QSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN P60137 Photosystem II reaction center protein M Oryza sativa Japonica Group 0.0036684509999999997 2 LEVO MEVNILAFIATALFILVPTAFLLIIYVKTVSQN P0C411 33 kDa subunit of oxygen evolving system of photosystem II Oryza sativa Japonica Group 0.026609848000000002 2 LEVO EGVPRRLTFDEIQSKTYMEVKGTGTANQCPTVEGGVDSFAFKAGKYNMKKFCLEPTSFTVKAEGVAKNAPPEFQKTKLMT RLTYTLDEIEGPLEVSSDGTIKFEEKDGIDYAAVTVQLPGGERVPFLFTIKNLVATGKPESFGGPFLVPSYRGSSFLDPK GRGGSTGYDNAVALPAGGRGDEEELAKENVKNASSSTGNITLSVTKSKPETGEVIGVFESVQPSDTDLGAKVPKDVKIQG VWYAQLES Q943W1 23 kDa subunit of oxygen evolving system of photosystem II Oryza sativa Japonica Group 0.020122321999999998 2 LEVO AYGEAANVFGKPKTNTEFIAYSGEGFKLLIPSKWNPSKEREFPGQVLRYEDNFDANSNVSVIINPTTKKTITEFGSPEEF LAQVDFLLGKQAYSGKTDSEGGFESDAVATANILESSAPVVGGKQYYSVTVLTRTADGDEGGKHQLITATVNDGKLYICK AQAGDKRWFKGARKFVESAASSFSVA Q8GTK4 Chlorophyll a-b binding protein, chloroplastic Oryza sativa Japonica Group 0.025938283 2 LEVO RPLWFPGAVAPDYLDGSLVGDYGFDPFGLGKPAEYLQFELDSLDQNLAKNNAGEIIGTRFETGEVKSTPFQPYTEVFGLQ RFRECELIHGRWAMLATLGALSVEWLTGVTWQDAGKVELVDGSSYLGQPLPFSISTLIWIEVLVIGYIEFQRNAELDPEK RLYPGGSYFDPLGLASDPEKKERLQLAEIKHARLAMVAFLGFAVQAAATGKGPLNNWATHLSDPLHTTIFDTFS Q6Z411 Chlorophyll a-b binding protein, chloroplastic Oryza sativa Japonica Group 0.023719937999999996 2 LEVO IGDELAKWYGPDRRIFLPEGLLDRSEVPDYLNGEVPGDYGYDPFGLSKKPEDFSKYQAYELIHARWAMLGAAGFIIPEAC NKFGANCGPEAVWFKTGALLLDGNTLNYFGNSIPINLIVAVAAEVVLVGGAEYYRIINGLDLEDKLHPGGPFDPLGLASD PDQAALLKVKEIKNGRLAMFSMLGFFIQAYVTGEGPVENLSKHLSDPFGNNLLTVISG Q53N83 Photosystem II reaction center protein T Oryza sativa Japonica Group 0.003692472 2 LEVO MEALVYTFLLVSTLGIIFFAIFFREPPKVPTK P0C427 Os02g0581100 protein Oryza sativa Japonica Group 0.0030096309999999996 2 LEVO VKRGTPEAKKKYAQICVTMPTAKVCHN Q0E032 Photosystem II 10 kDa polypeptide, chloroplastic Oryza sativa Japonica Group 0.01086142 2 LEVO PSLIIVAKKAKKIQTSQPYGPAGGVVFKEGVDASGRVAKGKGLYQFSNKYGANVDGYSPIYTPEEWSSTGDVYVGGKAGL LLWAITLAGILVGGAILVYNTSALA Q8H4P7 Photosystem II reaction center W protein, chloroplastic Oryza sativa Japonica Group 0.005866499 2 LEVO LVDERMSTEGTGLSLGLSNNLLGWILLGVFGLIWSLYTIYTSDLEEDEESGGLS Q5ZBY9 Os07g0673550 protein Oryza sativa Japonica Group 0.003927654 2 LEVO GSLTPSLKNFLLSIVSGGVVLVAIVGAVVAVSNFDPVKR Q7EXX2 Os08g0119800 protein Oryza sativa Japonica Group 0.004061776 2 LEVO DNRGLALLLPIAPAIAWVLYNILQPALNQLNRMRSE Q6ZJ41 Photosystem II reaction center protein Z Oryza sativa Japonica Group 0.0065827659999999994 2 LEVO MTIAFQLAVFALIVTSSVLVISVPLVFASPDGWSNNKNVVFSGTSLWIGLVFLVAILNSLIS P0C429 CHLOROPHYLL A 0.000893489 213 CLA CHLOROPHYLL B 0.000907472 92 CHL (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL 0.000568871 21 LUT (2R)-2,5,7,8-TETRAMETHYL-2-[(4R,8R)-4,8,12-TRIMETHYLTRIDECYL]CHROMAN-6-OL 0.000430706 2 VIV 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 66 LHG DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 13 DGD BETA-CAROTENE 0.000536873 23 BCR FE (II) ION 5.5845e-05 2 FE2 CHLORIDE ION 3.5453e-05 4 CL PHEOPHYTIN A 0.0008712 4 PHO CA-MN4-O5 CLUSTER 0.00033982699999999996 2 OEX 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 8 PL9 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL 0.0007951159999999999 23 SQD (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE 0.0006889719999999999 5 MGE ALPHA-LINOLENIC ACID 0.00027843 3 LNL BICARBONATE ION 6.1017e-05 2 BCT PROTOPORPHYRIN IX CONTAINING FE 0.000616487 2 HEM (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 6 XAT 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE 0.000704998 1 3PH singleParticle particle 7.3 ETHANE TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.4000000000000001 2.2 GATAN K3 (6k x 4k) 1.375 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 5XNL 2.89 FSC 0.143 CUT-OFF cryoSPARC 172752 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_68060.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 800 800 800 0 0 0 800 800 800 656.0 656.0 656.0 90.0 90.0 90.0 X Y Z 0.0 0.75299406 0.0005331093 0.008394583 0.82 0.82 0.82 0.0004 AUTHOR ::::EMDATABANK.org::::EMD-68060:::: emd_68060_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 419.84 419.84 419.84 90.0 90.0 90.0 X Y Z 0.0 2.5756319 0.0028210536 0.018688096 0.82 0.82 0.82 AUTHOR ::::EMDATABANK.org::::EMD-68060:::: emd_68060_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 419.84 419.84 419.84 90.0 90.0 90.0 X Y Z 0.0 2.8147674 0.0028250397 0.018736454 0.82 0.82 0.82 AUTHOR ::::EMDATABANK.org::::EMD-68060::::