2026-09-23 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY chem_comp chem_comp_atom em_admin pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_struct_conn_angle pdbx_validate_chiral struct_conn _chem_comp.formula _chem_comp_atom.pdbx_stereo_config _em_admin.last_update STRUCTURE_SUMMARY em_admin pdbx_modification_feature _em_admin.last_update _pdbx_modification_feature.ref_pcm_id EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update DATA_COLLECTION em_admin _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update PDBj PDBj 2022-07-01 2023-04-26 2023-04-26 2026-09-23 Japan Society for the Promotion of Science (JSPS) 21H04778 and 21H05040 Japan Chinese Academy of Sciences XDB37020101 and YSBR-015 China National Natural Science Foundation of China (NSFC) 31925024 China Ministry of Science and Technology (MoST, China) 2017YFA0503702 China Shan J Sheng X Ishii A Watanabe A Song C Murata K Minagawa J Liu Z Complex, Electron transport, Photosynthesis Ishii A Shan J Sheng X Kim E Watanabe A Yokono M Noda C Song C Murata K Liu Z Minagawa J Elife US 12 2023 36951548 doi:10.7554/eLife.84488 2050-084X 7yca FULLOVERLAP EMDB EMD-33737 associated EM volume

Cryo-EM structure of the PSI-LHCI-Lhcp supercomplex from Ostreococcus tauri

photosystem I-light-harvesting complex I-prasinophyte-specific Lhc protein (PSI-LHCI-Lhcp) supercomplex photosystem I-light-harvesting complex I-prasinophyte-specific Lhc protein (PSI-LHCI-Lhcp) supercomplex 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 Ostreococcus tauri OTH95 chloroplast thylakoid membrane Lhca1 Ostreococcus tauri 0.024128405999999998 1 LEVO MFAATRSFTQTVAPKTSVKARARVTARASARPMWFPGAEAPAHLRGDLPCDYGFDPLNLGEKPDNLARYREAELMHARWA MMGVAGAVGVEIAGQGDWASAQPTTWDATAKYLGNETHAPLFAVIGVNGVLVAFAESQRQAATGEARLYPGGSFDPAGLS KGKDFETLKRKELANGRVAMMAFFGIMAQHQADPSGPGPVKQLANHLADPWHVNVCTNPSAIPWL Q3B9U3 Chlorophyll a-b binding protein, chloroplastic Ostreococcus tauri 0.02640402 1 LEVO MWVDRGGDIGAHRRLKARATTTRASRRSVVVSAEAGAERPVWYPGKAPAPHLDGSLPGDFGFDPLSLSADPEMRKWMVQA ELQHARWAMLGVAGAVAPELLTKIGVADLPNWVDAGTYQYWAPAGPLFFIQMAMFNWAEVRRWQDMKNPGSMNTDPLFGY NSNDTNTDVGYPGGLFDKLGYAKDPAKAKELKLKEIKNGRLAMVAFLGICAQYVQTGQGPVENLFSHIASPGSVGYFGSQ GL A0A454XUD2 Chlorophyll a-b binding protein, chloroplastic Ostreococcus tauri 0.029432743999999997 1 LEVO MFATMNAIKITPFAKRQARRNVSVRAEEAEAAPAPVAKKTRNTEDLAPLYVLGNSEQSLSYLDGSLPGDYGFDPLGLSDP EGAGGFVNPKWLAYSELIHGRWAMLGVAGMVAPEVLGGMGIIPQETGLVWFKAGMIPAQGTYDYWASPFTIFWINAFLMN IAELRRAQDYWNPGSMGKQDFAGLEKMLGGSGDPAYPGGFFNFMKQGEKDMAAMKTKEIKNGRLAMMACFGCGAQACMTG EGPVKNLVDHVIDPFGHNLLVNFSQIGGVSPF Q3B9U5 Chlorophyll a-b binding protein, chloroplastic Ostreococcus tauri 0.025924592 1 LEVO MSAQFASTAVVGLRAPKTTKRSQRSVSVRASTQPMWFPGMDAPQHLKGELPGDYGFDPLNLGKEPKDLEWYVQAELQHGR WAMLGVAGAAAPEILTKMGISDLPNWHDAPNYQGYFTDATTLFWVQMLMMNWAEVRRWQDMRKPGSVNEDPAFSGNKLPS GIVGYPGGIFDPLGYAKGDLNKLKAKEIANGRLAMVAFAGIMVQYDHTGVGPVANLVAHMSDPAHNNVFQAKFIGF Q3B9V1 Chlorophyll a-b binding protein, chloroplastic Ostreococcus tauri 0.023401026999999998 1 LEVO MIAQRSALSARSIATPKATRRSAVVAAAADRKMWLPAPYKAPAHLDGSIAGDYGFDPLGLGTNPDRLKYYQEAELMNARW AMMAVAGIVGTEVAGIEPRWWEAGTEDYGFPPAALLAIQFPVMGYLENKRIQGWMATGSSGVNETFPFDPMGMGSKDANM KLKEIKNGRAAMIAFVGIVVQAIVYREGPVAALKDHISNPFGCNMATNIMNIPVNLA A0A090M1L8 Lhca6 Ostreococcus tauri 0.026742605 1 LEVO MFAQTAKTAIALKTTTARSTRASARSTRSVAVRAASDRELWYPGAVAPEYLNGSMAGDYGFDPLRLGANVETLPYLQEAE LMNGRWAMAATAGILFTDATGLPKWWEAGAADYGYDFQTLVAFQVVVMGVLEAFRVRGLMKTGESGVLNMFPFDPAGLDA PDKRVKEVKNGRLAMVAFLGMVSSYAVTGLSPLEALEAHMANPQAVNLFTSAVGGESVAFIAFLSCAPTFLLAQKTLGDG KEEFRPIPW A0A1Y5IA87 Photosystem I P700 chlorophyll a apoprotein A1 Ostreococcus tauri 0.083249305 1 LEVO MTISPPEREIKTVKIVVDRDPVPTSFEKWAKPGHFSRTLAKGPATTTWVWDLHADAHDFDSHTTDLEDISRKVFSAHFGQ LGVIFIWLSGMYFHGARFSNYEAWLSDPTHIKPSAQVVWPIVGQEILNGDVGGGFQGVQITSGFFQLWRGSGITSELQLY STAIGALICAGLMFFAGWWHYHKAAPKLEWFQNVESMMNHHLAGLLGLGSLAWAGHQIHIALPVNTLLDAGVDPKEIPLP HEFMLNRALMAELYPSFAKGLTPFFTFNWTEYSDFLTFRGGLNPVTGGLWLTDMAHHHLAIAVLFLVAGHQYRTNWGIGH SMKEILEAHKGPFTGEGHKGLYEILTTSWHAQLAINLALMGSLSIIVSHHMYSMPPYPYLATDYGTQLSLFTHHMWIGGF CICGAAAHAAIFMVRDYDPATNYNNVLDRVLRHRDAIISHLNWVCIFLGFHSFGLYIHNDTMSALGRPQDMFSDTAIQLQ PIFAQFVQHTHALAPELTAPTAAGSTSASWGGDIVAVGGKIAMMPISLGTSDFMVHHIHAFTIHVTVLILLKGVLFARSS RLIPDKANLGFRFPCDGPGRGGTCQVSAWDHVFLGLFWMYNSISIVIFHFSWKMQSDVWGSVTGNGVSHITGGNFAQSAN TINGWLRDFLWAQSSQVIQSYGSALSAYGLIFLGAHFIWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPAIQPRALSI TQGRAVGVAHYLLGGIATTWSFFLARIIAVG Q0P3K1 1.97.1.12 Photosystem I P700 chlorophyll a apoprotein A2 Ostreococcus tauri 0.081421508 1 LEVO MATKFPKFSQGLASDPTTRRIWFGIATAHDFETHDGMTEEKLYQKIFASHFGQLAIIFLWTSGNLFHVAWQGNFEKWGED PLHVRPIAHTIWDPHFGQPAVEAFTRGGASAPVNIAYSGVYQWWYTIGMRTNVDLYNGSLFLLFVAGLFLFAGWLHLQPT FAPAVSWFKNAESRLNHHLSGLFGVSSLAWTGHLVHVAIPASRGETVRWDNFLTTLPHPAGLAPFFTGQWAVYAQNPDTA GHIFGTSEGAGTAILTFLGGFHPQTQSLWLTDMAHHHLAIAVVFIIAGHQYRTNFGIGHSMKEILEAHTAPSGRLGAGHT GLFDTVNNSLHFQLGLALASVGVLCSLTAQHMYSMPPYAFLAQDFTTQAALYSHHQYIAGFIMCGAFAHGAIFFIRDYDP EANKGNVLARMLEHKEAIISHLSWVSLFLGFHTLGLYVHNDVMQAFGTPEKQILIEPVFAQWIQAAQGKALYGFDILLSG DNAATAAGNSIYLPGWLAGINSSTNSLFLPIGPGDFLVHHAIALGLHTTTLILVKGALDARGSKLMPDKKDFGYSFPCDG PGRGGTCDISAWDAFYLAVFWELNTVSWTVFYFHWKHLALWQGNSAQFDESSTYIMGWLRDYLWLNSSQLINGYNPFGMN SLSVWAWMFLFGHLIYATGFMFLISWRGYWQELIETLVWAHERTPLANFVKWNDKPVALSIVQARLVGLTHFAVGFVLTY AAFVIASTSGKFG Q0P3K2 1.97.1.12 Photosystem I iron-sulfur center Ostreococcus tauri 0.008751128 1 LEVO MSHAVKIYDTCIGCTQCVRACPTDVLEMVPWDGCKAGQIASAPRTEDCVGCKRCEAACPTDFLSVRVYLGSETTRSMGLA Y Q0P3P1 1.97.1.12 Photosystem I reaction center subunit II, chloroplastic Ostreococcus tauri 0.020560975 1 LEVO MSVTHAPARAVAKPTAMRTRKSARSATIVRAEEAKAKTESAAPAVWTAPKLDPNTPSPIFGGSTGGLLRKAQVEEFYVLT WEAKKEAIFEMPTGGAAIMRKGPNLLKLARKEQCLALLNTFRSKMKLDGCIYRVFPSGEVQYLHPKDGVYPEKVNKGRVG ANQNMRSIGKNTNPAKIKFQGKLGPFEV A0A1Y5I5Y8 Photosystem I reaction centre subunit IV Ostreococcus tauri 0.011278888999999999 1 LEVO MFACTKVQANVFAVKTTKTVRRSTVTRAEGEAAKPAAKPQVGPPRGTMVKILRPESYWFNDYGKVISVDQTGVRYPVVVR FEKVNYAGVSTNNYALDEVEY A0A454XT75 Photosystem I reaction center subunit III Ostreococcus tauri 0.024593398 1 LEVO MHAHAQAQLTSKVTVSGLKRSARVQTRAVKTVAHCSAVDFSKKAASLAVAAAVAAAPLVAVEEAFARDVQPYAGLTPCKT SKAFAKREKTELKALEKRLKKYDPESAPALALQATMEKTKTRFANYGESGLLCGKDGLPHLIVDGNLEHLGEFAIPGLGF LYVAGWIGYAGRSYIQENKTASKPTEGEIIIDVPKALGLMFQAGAWPLLAGLELKNGTLTAPESEITVSPR Q01B61 PsaG Ostreococcus tauri 0.014124991 1 LEVO MLARTALPTKTTASFNGRVAKQTRTAKRGAKVAARAFDDVNVVMSASNALALYLGRFVFLPYQRAQVERVGMPTQNGQTH FAAGDTRAEEASFITSTNDPAGFNLVDVFAWGSIGHAIGFLALASQSAQQML Q019T9 Photosystem I PsaH, reaction centre subunit VI Ostreococcus tauri 0.017797946999999998 1 LEVO MAHVKVHTWTQIARNTTTPPTTTTTTTRERPARQSSMVAHAKTTAFATGAALARSTPTTRRARATVMTRAKYGDESVYFD LSDVEATTGSWDVYGVDSASRYPEQQAAFFEAAAQGLGRREAVYSVLAVSAGLLTVAYGVKGAKDAKLPITVGPQQPAQV GPRDRI A0A096PAU9 Photosystem I reaction center subunit VIII Ostreococcus tauri 0.0037665729999999996 1 LEVO MAASLLPSIFVPLVGLVFPAVAMASLFLYIEKEQV Q0P3K0 Photosystem I reaction center subunit IX Ostreococcus tauri 0.004731595 1 LEVO MKNFQIYLSTAPVLAAVWFTVLAGILIELNRFFPDALSFPLT Q0P3J4 Photosystem I PsaG/PsaK protein Ostreococcus tauri 0.013573482999999999 1 LEVO MHATVAARPSIVSAKTSLSSTDALKRASAVAQRTKTRDVTVRADWSIGSTENMIVCFNTTAILGAMRFGLMPSVKKNFNG ASSHTAMVEQANAKTIGSRDPSGFTAVDVLAGGSLATIISAGEILAGQVPY A0A096P8E8 PSI subunit V Ostreococcus tauri 0.021526773 1 LEVO MVLASKLTLDVRSCIGAKSLRTERPRNSAIGSNKTSRRQTKVSASSDKVQIVKPINGDPFIGMLETPVTSSPDVANFLSN LPAYRTGVAPLLRGVEVGLAHGFFVTGPFIKLGPLRSTDAAELAGCLSGAGLVLILTACLSIYGATAFQREEVVGLKTLS GRTIAKDPLQSSEGWASFTSGWLVGGLSGVAWSYVLTQVLPYYS A0A090M7B0 Photosystem I reaction center subunit XII Ostreococcus tauri 0.003413078 1 LEVO MPLSDTQVFTALFVALITGILSLRLGTQLYK Q0P3J8 Photosystem I PsaN, reaction centre subunit N Ostreococcus tauri 0.014405324 1 LEVO MYTVCGANIIAAKAPTAAKKQDKVKRAVSLGLAGLAAATVSVAPAHADLTADLLARTEANKSLNDQKRAATSSANFERSR LVTDGFCQFPQNIFGCQNAAEKGSVKFLSDDMAIECEGTADGKTCSSKAPGAYPSFLGL A0A090N3J0 PsaO Ostreococcus tauri 0.015020308 1 LEVO MLALAPINVQRRSPLGVSARGRKTQSKARFAVKVNAANADLKFDDDWKKSNVAVHLASLFGWVIPSASPCPAFPDNASLF KVFSDRISENLAHFPTGPSADDPIWLYMLTWHMGLFACMMFGQIGVQARKQGYFGN A0A096P9N0 Chlorophyll a-b binding protein, chloroplastic Ostreococcus tauri 0.024689807 8 LEVO MSALLASSFVSRVAAFKAQKVQNKSVSTTVKADIYPEFGTYPGGGESPIIPFGSEKNAEREVIHGRWAMLGVTGAWAAEN GTGIPWFTAGTLCTPDDCTAVADKFPGAVAPLAPEGSGYPSFWNVLIIEIVLVGAAEAYRTGISDSPFDDGLTVGDVNPG GRFDPLGLAESGDLEELKIKELKHCRLSMFAWLGCIFQALATQEGPIANWQSHVADPVHSNVLTNAAKGFGFY Q3B9U7 Chlorophyll a-b binding protein, chloroplastic Ostreococcus tauri 0.024161298999999997 1 LEVO (ACE)RR(TPO)KASVPAKRSAFKANKFGSLAPPDLYPEFGTYPGGGESPVIPFGSEKNAEREIIHGRWAMLGVTGAWAA ENGTGIPWFTAGTLCTPDDCTAVADKFPGAVAPLAPAGSGYPNFWAVLAIEIFLVGSAECYRTGLFENPFPELTQGDVTP GGRFDPLGFAEAGDLEELKIKELKHSRLAMFAWLGCIMQALATQEGPIANWTAHVADPIHANVLTNAAKGFKFY A0A090LYE8 CHLOROPHYLL B 0.000907472 60 CHL CHLOROPHYLL A 0.000893489 245 CLA (3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-1-[(1~{S},4~{S})-2,2-dimethyl-6-methylidene-1,4-bis(oxidanyl)cyclohexyl]-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-2-one 0.00060087 23 IWJ (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-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 10 LHG (1~{S})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaenyl]cyclohex-3-en-1-ol 0.000570887 39 Q6L BETA-CAROTENE 0.000536873 30 BCR 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 11 LMG 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL 0.0007951159999999999 2 SQD CHLOROPHYLL A ISOMER 0.000893489 1 CL0 PHYLLOQUINONE 0.000450696 2 PQN IRON/SULFUR CLUSTER 0.00035163999999999996 3 SF4 DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 2 DGD (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 6 NEX Chlorophyll c2 0.000608926 9 KC2 water 1.8015e-05 4 HOH singleParticle particle 6.5 Quantifoil R1.2/1.3 NITROGEN 100 277 FEI TITAN OTHER BRIGHT FIELD FIELD EMISSION GUN 300 1.8 2.2 GATAN K2 BASE (4k x 4k) 60.0 1

The selected images were normalized

5288217

Template picker was used to automatically select particle images

cryoSPARC 3.3.1 MotionCorr2 1.3 NONE EMD-6932 C1 2.94 FSC 0.143 CUT-OFF RELION 3.1 80366 MAXIMUM LIKELIHOOD RELION 3.1 PROJECTION MATCHING RELION 3.1 1 80573.0 5ZJI A PDB experimental model 5ZJI B PDB experimental model 5ZJI C PDB experimental model 5ZJI D PDB experimental model 5ZJI E PDB experimental model 5ZJI F PDB experimental model 5ZJI G PDB experimental model 5ZJI H PDB experimental model 5ZJI I PDB experimental model 5ZJI J PDB experimental model 5ZJI K PDB experimental model 5ZJI L PDB experimental model 5ZJI O PDB experimental model 7D0J Q PDB experimental model 7D0J P PDB experimental model RIGID BODY FIT

Initial local fitting was done using Chimera and then Wincoot was usd for flexible fitting

Correlation coefficient REAL 110.966999999999999 emd_33737_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 399.36 399.36 399.36 90.0 90.0 90.0 X Y Z -0.01932289 0.0777593 0.000031335705 0.0020508382 1.04 1.04 1.04 AUTHOR ::::EMDATABANK.org::::EMD-33737:::: emd_33737_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 399.36 399.36 399.36 90.0 90.0 90.0 X Y Z -0.021038175 0.08015759 0.000031412455 0.0020558576 1.04 1.04 1.04 AUTHOR ::::EMDATABANK.org::::EMD-33737::::