Cryo-EM structure of PpPSI-L

2026-09-23 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update 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 DATA_COLLECTION em_admin _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update PDBj PDBj 2022-12-21 2023-08-02 2023-08-02 2026-09-23 National Natural Science Foundation of China (NSFC) China Cryo-EM structure of PpPSI-L Li M Pan XW Sun HY Lhcb9, PSI, PHOTOSYNTHESIS Sun H Shang H Pan X Li M Structural insights into the assembly and energy transfer of the Lhcb9-dependent photosystem I from moss Physcomitrium patens. Nat.Plants UK 9 1347 1358 2023 37474782 doi:10.1038/s41477-023-01463-4 2055-0278 EMD-35026 other EM volume

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EMD-35027 other EM volume

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EMD-35033 other EM volume

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EMD-35034 other EM volume

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8htu FULLOVERLAP EMDB EMD-35018 associated EM volume

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EMDB EMD-35026 other EM volume

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EMDB EMD-35027 other EM volume

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EMDB EMD-35028 other EM volume

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EMDB EMD-35033 other EM volume

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EMDB EMD-35034 other EM volume

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photosystem I from Physcomitrium patens photosystem I from Physcomitrium patens 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 Physcomitrium patens Chlorophyll a-b binding protein, chloroplastic Physcomitrium patens 0.028403947 3 LEVO MAAATAMHSTTLAGQSLLKPVNELSRKVGSSEARVTMRR(TPO)VKSTSDSIWYGADRPKYLGPFSGETPSYLTGEFAGD YGWDTAGLSSDPETFARNRELEVIHARWAMLGALGCLTPELLAKSGVKFGEAVWFKAGAQIFSEGGLDYLGNPSLVHAQS ILAIWASQVVLMGAVEGYRVAGGPLGEITDPIYPGGSFDPLGLADDPDTFAELKVKEIKNGRLAMFSMFGFFVQAIVTGK GPLENLNDHLADPVANNAWAYATNFVPGN A9RT62 Chlorophyll a-b binding protein, chloroplastic Physcomitrium patens 0.025931562000000002 2 LEVO MASAMATAAAAQVSRVVTGVATAQKSSFFAGSSSVSLLGCSNGSRVCMAEWLPGNPRPSYLDGSAPGDFGFDPLGLGEVP ENLERFKESELIHARWAMLAVPGVLIPEALGYGNWVSAQKWAATPGGQATYLGNPVPWGNLPVILAIEFLAIAFAESQRN GEPDPEKRKYPGGAFDPLGFSKGANLEELKLKEIKNGRLALVAFLGFAVQAIAYPGTGPLENLKTHLADPWHNTIAHVII PRSVL A0A2K1JLZ3 Chlorophyll a-b binding protein, chloroplastic Physcomitrium patens 0.029036997999999998 2 LEVO MASAVCASSNVAVVAGPSTSKVVNSAGPARTSLLAGRVRRVTRIAASPQAEAPVPAQPSLPNNDRPLWFPGSQPPEWLDG SLPGDFGFDPLGLGSDPELLKWFVQAELVHCRWAMLGAAGIFIPEALTKAGILNTPSWTVAGDQQYFTDATTLFVIEIIL FAWAEGRRWADIINPGCVNVDPVFPNNKLTGTDVGYPGGLWFDPLGWGQTGDAAKLKDLRTREIKNGRLAMLAVLGAVVQ ANYTHTGPIDNLLAHLADPGHNTIFALSNLVGK A9TJ06 Chlorophyll a-b binding protein, chloroplastic Physcomitrium patens 0.034673801 2 LEVO MRTFNLTHLSFPSIGVFLSPLSCIESRVAGVQVCSAMATRVAAGCAVSSFAAKVSPSAFEGKRSAVFGTNLPSTFYVVSK KASSSAKTVVTKAQLSPTGGSKRSLIFASKQSLSYLDGTLPGDYGFDPLGLMDPEGAGGFIDPQWLPYAEIINGRFAMLG AAGAIAPEVLGRIGLIPQETAIPWFQSGVIPPVGNYSYWADPYTLFVLEMALMGFAEHRRAQDYYKPGSMGKQYFLGLEK FLGGSGNPAYPGGPIFNFLGFGKNEKELQELKVKEVKNGRLAMMAVLGYFTQAIFTGVGPFQNLLDHLADPVHNNVLTNL KIH A0A2K1IB10 Chlorophyll a-b binding protein, chloroplastic Physcomitrium patens 0.028818881 2 LEVO MASAVCASSSVAAVAAPSTSKVVSNVGSARTSFLAGRALRTTQVCGAAKGDMTVSATLTGNKTDRPLWLPGSEAPKWLDG SLPGDYGFDPLDLAAEPGRLNWMVQAELVHCRWAMLGAAGIFIPELLTKIGILNTPSWYKAGDATYFADQGTLFIVELLL MAWAESRRWADIARPGSVNTDPIFPNNKLTGTDVGYPGGLWFDPLGWGSGSEDKLKEIRTKEVKNGRLAMLAVLGAFVQA NVTHVGPIDNLFAHLADPYHTTILQSLFGK A0A2K1K0E4 Photosystem I P700 chlorophyll a apoprotein A1 Physcomitrium patens 0.083226508 1 LEVO MTIRSPEPEVKIMVEKDPVKTSFEKWAKPGHFSRTLAKGPNTTTWIWNLHADAHDFDSHTNDLEEISRKVFSAHFGQLAV IFIWLSGMYFHGARFSNYEAWLSDPTHIKPSAQVVWPIVGQKILNGDVGGGFQGIQITSGFFQLWRASGITSELQLYTTA IGGLIFAALMLFAGWFHYHKAAPKLAWFQNVESMLNHHLAGLLGLGSLAWAGHQVHVSLPINRLLDAGVDPKEIPLPHEF ILNRDLLAQLYPSFSKGLTPFFTLNWSEYSDFLTFRGGLNPVTGGLWLTDTAHHHLAIAVLFLVAGHMYRTNFGIGHSMK EILEAHKGPFTGEGHKGLYEILTTSWHAQLAINLAMLGSLTIIVAHHMYAMPPYPYLATDYATQLSLFTHHMWIGGFLVV GAAAHAAIFMVRDYDPTTQYNNLLDRVLRHRDAIISHLNWVCIFLGFHSFGLYIHNDTMSALGRPQDMFSDTAIQLQPVF AQWIQNTHALAPSLTAPNATASTSLTWGGGDLVAVGGKVALLPIPLGTADFLVHHIHAFTIHVTVLILLKGVLFARSSRL IPDKANLGFRFPCDGPGRGGTCQVSAWDHVFLGLFWMYNAISVVIFHFSWKMQSDVWGSISDQGVVTHITGGNFAQSSIT INGWLRDFLWAQASQVIQSYGSSLSAYGLLFLGAHFVWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPAIQPRALSIV QGRAVGVAHYLLGGIATTWAFFLARIISVG Q8MFA3 1.97.1.12 Photosystem I P700 chlorophyll a apoprotein A2 Physcomitrium patens 0.08244775 1 LEVO MASRFPKFSRGLSQDPTTRRIWFGIATAHDFESHDDMTEERLYQKIFASHFGQLAIIFLWTSGNLFHVAWQGNFEAWGQD PLHVRPIAHAIWDPHFGQPAVEAFTRGGASGPVNIAYSGVYQWWYTIGLRTNQDLYGGSIFLLFVSALFLIAGWLHLQPK WKPSVSWFKNAESRLNHHLSGLFGVSSLAWTGHLVHVAIPESRGEHVRWNNLLTALPHPQGLGPFFAGQWNVYAQNPDSN SHLFGTSEGAGTAILTFLGGFHPQTQSLWLTDMAHHHLAIAVIFIIAGHMYRTNFGIGHSMKEILEAHTPPGGRLGRGHK GLYDTINNSLHFQLGLALASLGVITSLVAQHMYSLPPYAFLAQDFTTQAALYTHHQYIAGFIMTGAFAHGAIFFIRDYNP EQNKDNVLARMLEHKEAIISHLSWASLFLGFHTLGLYVHNDVMLAFGTPEKQILIEPVFAQWIQSAHGKALYGFDVLLSS ADSPAFNAGQTLWLPGWLDAINNNSNSLFLTIGPGDFLVHHAIALGLHTTTLILVKGALDARGSKLMPDKKEFGYSFPCD GPGRGGTCDISAWDAFYLAVFWMLNTIGWVTFYWHWKHITLWQGNVAQFNESSTYLMGWLRDYLWLNSSQLINGYNPFGM NSLSVWAWMFLFGHLVWATGFMFLISWRGYWQELIETLAWAHERTPLANLVRWKDKPVALSIVQARLVGLAHFSVGYIFT YAAFLIASTSGKFG Q8MFA2 1.97.1.12 Photosystem I iron-sulfur center Physcomitrium patens 0.008781153 1 LEVO MAHSVKIYDTCIGCTQCVRACPTDVLEMVPWDGCKASQIASAPRTEDCVGCKRCESACPTDFLSVRVYLGAETTRSMGLA Y Q6YXQ2 1.97.1.12 Photosystem I reaction center subunit II, chloroplastic Physcomitrium patens 0.022183309000000002 1 LEVO MAALAATSAASIALAIPQASSGASTSRSVNLRLSGIQGQKLAAVCNGSRVVAKAAGAAPDATAEAPKGFTPPTLNADTPA PIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRSGPNLLKLARKEQCLALGARLRTKFKIQYQFYRVFPN GEVQYLHPKDGVYPEKVNAGRTAVGVNNRSIGQNANPAELKFAHKQAYDL A9REG3 Photosystem I reaction center subunit IV, chloroplastic Physcomitrium patens 0.013919796 1 LEVO MSTAVSSFVGVASNAVAATGAATSSMFSTKVPCRPLSMVVSGRNSARLVVRAEEAAAAPPAKKEAQPVIGPKRGSIVKVL RRESYWFNDTGKVVAVDQAPGVRYPVVVRFDKVNYAGVSTNNYSPDELEQSA A0A2K1IHL7 Photosystem I reaction center subunit III Physcomitrium patens 0.026112318 1 LEVO MASVTMAAIAPAGLVAPLCKDVSSRTAISGARASVFVKSSKARIVCSTSADETSTVAETAGKFATALALAAVVGSSDFVV PDARADVAGLTPCKESKGFAKRQKQEIKKLEGRLKLYAPDSAPALAINATIEKTKRRFEFYGNQGLLCGTDGLPHLIVDG DQAHLGEFVYPGLVFLYIAGWIGWVGRAYLIDVRTSKKPTEKEIIIDVPLALRIMSKGLTWPVAAIGELRSGKLVEKSSN ITVSPR A0A2K1IN36 Photosystem I reaction center subunit V, chloroplastic Physcomitrium patens 0.016231396 1 LEVO MASCAASMTGVAASSLSLKANFSGLRRGTKVDSIAMSRSSSFASKTAIAKSSGKVTCEANTALTITLSTGALLFLGRFVF LPFQRDNVSRQGLPVQNGVTHFDAGDSRAQEVTSFLKTNDPAGFTIVDVLAWGALGHAVGFFILATINNGYNPQF A0A2K1JC42 Photosystem I reaction center subunit VI, chloroplastic Physcomitrium patens 0.014506459 1 LEVO MAAASATMAVSGLAGSSLAGQKFAIAPAKSVSVRSPSKVGAISAKYGEKSVYFDLGEIDNTTGNWDLYGNDDPNRYNGFQ NKFFETFAGAFTKRGLLLKFLVLGGATTIGYLGSTSSGDLLAIKNGPKQAPIMGPRGRK A0A2K1JDR4 Photosystem I reaction center subunit VIII Physcomitrium patens 0.004017786999999999 1 LEVO MTASYLPSIFVPLIGLVFPAITMASLFIYIEQDEII Q6YXR3 Photosystem I reaction center subunit IX Physcomitrium patens 0.00459746 1 LEVO MQDVKTYLSTAPVLATLWFGFLAGLLIEINRFFPDALVLPL Q6YXM2 Photosystem I subunit X Physcomitrium patens 0.013278443999999999 1 LEVO MAAMATTMSVATVRQFEGLKATTSSFSKPLPSLALRKTAGKGALGARCDYIGSSTNLIMVASTTLMLFAGRFGLAPSANR KSTAGLKLVDRDSGLQTGDPAGFTATDTLACGALGHVIGVGIVLGLKATAGL A0A2K1KU02 PSI subunit V Physcomitrium patens 0.023530298999999998 1 LEVO MAAAAMTRAGGLLAMERVQRVSKTTGAVSNRTFLGNVRGLRATSAPQALRVKVMAVRAGAEKYQVIEPLNGDPFIGGFET PVTSSPLIAWYLSNLPAYRTAVAPLLRGVEIGLAHGYLLVGPFVLAGPLRNSAVRGEAGSLAAAGLVTILTMCLTIYGIA SFKEGEASKAPSLTLTGRQKEADKLQTAEGWASFTGGWFFGGLSGVAWAYFLLYVINLPYPVK A0A7I4A0Q6 Photosystem I reaction center subunit XII Physcomitrium patens 0.0034120509999999997 1 LEVO MTSISDSQIIVALVSAFITGILALRLGKSLYQ Q6YXK4 Photosystem I subunit O Physcomitrium patens 0.015393112999999998 1 LEVO MAMTATSMAMPAVAGLGSSSILARRSPKLQLTSAFVGGAIKVNKPLCMSRVTCFNRDWLRKDLSVIGFGLIGWLAPSSLP VINGNSLTGLFLGSIGPELAHFPTGPALTSPFWLWMITWHVGLFIVLTLGQIGFKGRQDGYWN A0A2K1JDF1 Chlorophyll a-b binding protein, chloroplastic Physcomitrium patens 0.033175734 1 LEVO MASMAIQGVVAPAVGAFGSSKCFQKKPSSISSSSWTCQAVSKGEGTADAPTVSLEGVINAVQQAPSADPAPEALLAESTS NGSTATMTGIAEWYKVYGKSVAPDQDARAPYYGPNRPLWKGPFTKPKDVPEYLKGEYPGDYGCDIFKLARLPANYARLRT QELMNGRWAMLGITGCLTPELINSNSTPGFEPVWFNTGAQIFSDAGIDYLGVPGFINAHSLFAVIVVQALLMGLAEYARI KFVPEGADPFYPGGKTFDPLGFSSDPEILAELKVKEIKNGRLAMMAMAGLFAQGAVTGVSPLQNLHDWLHL A0A2K1KKR9 CHLOROPHYLL B 0.000907472 49 CHL CHLOROPHYLL A 0.000893489 221 CLA (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL 0.000568871 17 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 11 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 4 NEX 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 15 LHG BETA-CAROTENE 0.000536873 33 BCR 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 6 LMG PHYLLOQUINONE 0.000450696 2 PQN IRON/SULFUR CLUSTER 0.00035163999999999996 3 SF4 DODECYL-BETA-D-MALTOSIDE 0.000510615 4 LMT DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 1 DGD water 1.8015e-05 2 HOH singleParticle particle 6.5 ETHANE FEI TITAN KRIOS OTHER OTHER OTHER 300 1.5 2.5 GATAN K2 SUMMIT (4k x 4k) 60.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 7KSQ

5ZJI 7D0J

2.87 FSC 0.143 CUT-OFF 144586 PROJECTION MATCHING PROJECTION MATCHING emd_35018.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 332.8 332.8 332.8 90.0 90.0 90.0 X Y Z -0.03939079 0.2498145 0.0005223833 0.0049055596 1.04 1.04 1.04 0.0188 AUTHOR ::::EMDATABANK.org::::EMD-35018:::: Combining three focused refinement maps, smPSI, LHCII and outer LHCI plus Lhcb9