PSI-4 LHCI dimer supercomplex from M. polymorpha

2026-02-18 REL PDBj 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 PDBj PDBj 2025-02-10 2026-02-18 2026-02-18 2026-02-18 Japan Society for the Promotion of Science (JSPS) JP22H04916 Japan PSI-4 LHCI dimer supercomplex from M. polymorpha Tsai P-C La Rocca R Shen J-R Akita F Photosystem I, PHOTOSYNTHESIS Tsai PC La Rocca R Motose H Shen JR Akita F Structural study of monomeric and dimeric photosystem I-LHCI supercomplexes from a bryophyte. Commun Biol UK 9 146 146 2026 41644713 doi:10.1038/s42003-026-09631-w 2399-3642 9luu FULLOVERLAP EMDB EMD-63405 associated EM volume

Photosystem I-4 LHCI dimer supercomplex from liverwort Photosystem I-4 LHCI dimer supercomplex from liverwort 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 Marchantia polymorpha Photosystem I P700 chlorophyll a apoprotein A2 Marchantia polymorpha 0.08248468799999999 2 LEVO MASRFPKFSQGLSQDPTTRRIWFGIATAHDFESHDDMTEERLYQKIFASHFGQLAIIFLWTSGNLFHVAWQGNFEAWGQD PLHVRPIAHAIWDPHFGQPAVEAFTRGGASGPVNIAYSGVYQWWYTIGLRTNQDLYNGALFLVILSSISLIAGWLHLQPK WKPKVSWFKNAESRLNHHLSGLFGVSSLAWTGHLVHVAIPESRGEHVRWDNFLTKLPHPEGLGPFFAGQWNVYAQNVDSS NHAFGTSQGAGTAILTFIGGFHPQTQSLWLTDIAHHHLAIAVVFIIAGHMYRTNFGIGHSIKEILETHTPPGGRLGRGHK GLYDTINNSLHFQLGLALASLGVITSLVAQHMYSLPPYAFLAQDFTTQAALYTHHQYIAGFIMTGAFAHGAIFFIRDYNP EQNKDNVLARMLEHKEAIISHLSWASLFLGFHTLGLYVHNDVMLAFGTPEKQILIEPIFAQWIQSAHGKALYGFDVLLSS TNNPAFNAGQSIWLPGWLDAINNNSNSLFLTIGPGDFLVHHAIALGLHTTTLILVKGALDARGSKLMPDKKEFGYSFPCD GPGRGGTCDISAWDAFYLAVFWMLNTIGWVTFYWHWKHITLWQGNAAQFNESSTYLMGWLRDYLWLNSSQLINGYNPFGM NSLSVWAWMFLFGHLVWATGFMFLISWRGYWQELIETLAWAHERTPLANLVRWKDKPVALSIVQARLVGLAHFSVGYIFT YAAFLIASTSGKFG A0A3Q9R072 1.97.1.12 Photosystem I iron-sulfur center Marchantia polymorpha 0.008866216 2 LEVO MAHAVKIYDTCIGCTQCVRACPTDVLEMIPWDGCKANQIASAPRTEDCVGCKRCESACPTDFLSVRVYLGDETTRSMGLS Y A0A3Q9R1I6 1.97.1.12 Photosystem I reaction center subunit II, chloroplastic Marchantia polymorpha 0.022614096 2 LEVO MASLACTSAVAAVAATGPVAKIENGSTNVARSLAMAPLKASSLHGQKMSVASSAARVTMAAAGKAPAAEAPAGFTPPELK ADTPSPIFGGSTGGLLRKAQVEEFYVITWDSPKEQIFEMPTGGAAIMRSGPNLLKLARKEQCLALGTALRTKFKIKYQFY RVFPNGEVQYLHPKDGVYPEKVNAGRTAVGFNSRSIGKNKNPAEIKFGKAPAFEL A0A2R6W6G7 Photosystem I reaction centre subunit IV Marchantia polymorpha 0.013821722 2 LEVO MAAAASSMLAMVAAPAAGLSSNVSQTRVQIRRVGAARFPRFTIRAADAPAEPAAAAPAAAPEKAAPPPPFGPKRGSTVKI MRPESYWFNETGTVVSVDQTPGLRYPVVVRFTKCNYAGVNTNNYGIDEVSSV A0A2R6WSQ6 Photosystem I reaction center subunit III Marchantia polymorpha 0.026025164 2 LEVO MATVSMAAISPAGLVAPLNVSSKSTFAASTKVSAFVKNVRARTVCSASAEKEQTVGETAGKIATALALAAVVGTASFVAP EDAMADVAGLTPCKESKAFAKREKNEIKALEKRLKLYGADSAPALAIKATVEKTKRRFAFYGNEGLLCGTDGLPHLIVDG DQAHLGEFVYPGVVFLYIAGWIGWVGRSYLIAIRGEKKPTEKEIIIDVPLATSLLWKGLTWPVAALSELRTGKLIEDASN ITVSPR A0A2R6WM91 Photosystem I reaction center subunit V, chloroplastic Marchantia polymorpha 0.016912247999999998 2 LEVO MASCTAQIAVAAGVPALAARSKSIRASSSQVSFSGRNMVSCVSISNRSWESQTKLARANARTVCADTSLVISLSTGALLF LGRFVLLPFQRKQVSQAGLPRQNGVTHFEAGDARAQEVSSLMKTNDPAGFTIVDLLAWGALGHAVGFFILATASNGYDPT F A0A2R6X3Q4 Photosystem I reaction center subunit VI, chloroplastic Marchantia polymorpha 0.014660665 2 LEVO MASIVAVAGPSVVAGLGSSSLSGQKLRVSTRSFSVRAAPSVGVASAKYDAGNSKYFDLEDLGNTTGAWDLYGSDQLSPYN GMQSKFFETFAYPLTKRGILLKLGLLGGALALGFASSSATGDILAIKKGPQGPPQMGPRNRI A0A2R6XLB4 Photosystem I reaction center subunit VIII Marchantia polymorpha 0.004017786999999999 2 LEVO MTASYLPSIFVPLVGLIFPAITMASLFIYIEQDEIL P12185 Photosystem I reaction center subunit IX Marchantia polymorpha 0.00477865 2 LEVO MQDVKTYLSTAPVLATLWFGFLAGLLIEINRFFPDALVLPFF P12191 PSI subunit V Marchantia polymorpha 0.023152728999999997 2 LEVO MATAAMVRAGGLLSLQQTATKNVVRSSFVGSAAPLRFRSASSSVSVRPMSIRAGATTEGKYQVVEPLNGDPFVGGLETPV TSSPLIAWYLSNLPAYRTAVSPLLRGVEVGLAHGFLLVGPFVKTGPLRNTDIAGPAGSFAAAGLVVILSVCLTMYGIAQF KEGAASIAPSLTLSGRKKEADKLQTAQGWASFSGGFFFGGLSGVYWAYFLLYVVNLPYFVK A0A2R6WE99 Photosystem I reaction center subunit XII Marchantia polymorpha 0.003568273 2 LEVO MTSISDSQIIVILLSVFITSILALRLGKELYQ P31590 Photosystem I P700 chlorophyll a apoprotein A1 Marchantia polymorpha 0.083299375 2 LEVO MTIRSPEPEVKIVVEKDPVKTSFEKWAKPGHFSRTLAKGPSTTTWIWNLHADAHDFDSHTNDLEEISRKVFSAHFGQLAI IFIWLSGMYFHGARFSNYEAWLSDPTHIKPSAQVVWPIVGQEILNGDVGGGFQGIQITSGFFQLWRASGITSELQLYSTA IGGLVFAALMLFAGWFHYHKAAPKLAWFQDVESMLNHHLAGLLGLGSLSWAGHQVHVSLPINQLLDAGVDPKEIPLPHEF ILNRDLLAELYPSFAKGLTPFFTLNWSEYSDFLTFRGGLNPVTGGLWLTDTAHHHLAIAVLFLVAGHMYRTNWGIGHSFK EILEAHKGPFTGEGHKGLYEILTTSWHAQLALNLAMLGSLTIIVAHHMYAMPPYPYLATDYGTQLSLFTHHMWIGGFLIV GAAAHAAIFMVRDYDPTTQYNNLLDRVLRHRDAIISHLNWVCIFLGFHSFGLYIHNDTMSALGRPQDMFSDTAIQLQPVF AQWIQNTHALAPNFTAPNALASTSLTWGGGDVIAVGSKVALLPIPLGTADFLVHHIHAFTIHVTVLILLKGVLFARSSRL IPDKANLGFRFPCDGPGRGGTCQVSAWDHVFLGLFWMYNSISVVIFHFSWKMQSDVWGTISEEGVVTHITGGNFAQSAIT INGWLRDFLWAQASQVIQSYGSSLSAYGLLFLGAHFVWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPAIQPRALSIT QGRAVGVAHYLLGGIATTWAFFLARIIAVG A0A3Q9R2J6 1.97.1.12 Chlorophyll a-b binding protein, chloroplastic Marchantia polymorpha 0.028576648 2 LEVO MATAVCTTSRIASIAPSTSATKAVSSGSAVKAAFFGKTLRSAKVSAVSKASFSVRAQATERPLWFPGSTAPEWLDGSLPG DFGFDPLGLGSEPELLKWFVQAEIVHCRWAMLGAAGIFIPELLTKIGILNTPSWYTAGEQTYFADQTTLFIVELLFMGWA EGRRWADILKPGSVNTDPVFPNNKLTGTDVGYPGGFWFDPLGWGAGGAAKVKELRTKEIKNGRLAMLAVMGAWFQAVYTG TGPIDNLFAHLADPGHATVFAALDKLQ I7JD56 Chlorophyll a-b binding protein, chloroplastic Marchantia polymorpha 0.030133443 2 LEVO MATTVACRAVAGAVFAPAQEQRLMGGNALRVSFAPIGTSNARSSIVVRASSDKPVKANRQLIFASEQSLSYLDGSLPGDY GFDPLGLSDPQGAGGFIDPNWLRYAEIINGRFAMLGAAGAIAPEIFGKIGLIPQETAIPWFQTGVIPPLGQYSYWADPYT LFVLEMALMGFAEHRRAQDYYKPGSMGKQYFLGFEKVLGGSGDPAYPGGPLFNFLGFGRDEKSMKDLKVKEVKNGRLAML AVLGYFIQAIFTGVGPFQNLLDHLSDPANNNVLTNLKIH I7KJM4 Chlorophyll a-b binding protein, chloroplastic Marchantia polymorpha 0.027114066 2 LEVO MASVSMQAMSVSSAVCKTSFLSGTSSTRFSRNVQVAAAPISSQSLKVEAKKGEWLPGLPSPAYLNGSLAGDNGFDPLGLA EDPAALNWYVQAELQNGRWAMLGVAGMLVPEVLTKIGLINAPLWYDAGKVEYFAPASTLFVIEFILFHYVEIRRWQDIKY PGSVSQDPFFKSYKLPPGDVGYPGGIFNPLKFPANQEYKEKEIANGRLAMLAFLGMLVQSKLTGAGPFENLLTHLADPWH TTIVQTLAN I7IIM0 Chlorophyll a-b binding protein, chloroplastic Marchantia polymorpha 0.026038800999999997 2 LEVO MAAATMACVGLSAPALLSGAQRTKFFSGHVSSLSTVSNGSRVSMSSEWMPGQPRPAYLDGSSPGDFGFDPLGLAEVPENF ARYKESELIHCRWAMLAVPGVLIPEALGLGNWVSAQQWAATPGGQATYLGNPVPWGTLPIILAIEFLAVAFVEAKRGEEP DHEKRKYPGGPFDPLGFAKDPKKLEEYKLKELKNGRLALLAFLGFSVQAIAYPGTGPLENLASHLSNPWANNIANIIIPR SVL I7JWJ2 PSI-K Marchantia polymorpha 0.013483683 2 LEVO MATSIVSASAVVAAPAREFAGLRATTSFGKVQNVAMLPKSVNGKGALGARCDYIGSSTNLIMVASTTLMLFAGRFGLAPS ANRKALSGLKLVDRDSGLQTGDPAGFTATDTLACGVMGHIIGVGIVLGLKATGGL A0A2R6W993 CHLOROPHYLL A 0.000893489 276 CLA PHYLLOQUINONE 0.000450696 4 PQN BETA-CAROTENE 0.000536873 42 BCR DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 2 DGD EICOSANE 0.000282547 4 LFA 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 10 LMG IRON/SULFUR CLUSTER 0.00035163999999999996 6 SF4 (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL 0.000568871 20 LUT CHLOROPHYLL A ISOMER 0.000893489 2 CL0 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 12 LHG DODECYL-ALPHA-D-MALTOSIDE 0.000510615 6 LMU CHLOROPHYLL B 0.000907472 28 CHL singleParticle particle 7.5 Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY GLOW DISCHARGE 10 OTHER 0.007

10 mA

ETHANE FEI VITROBOT MARK IV

1.46 mg Chl a per mL

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 0.6 1.8 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN VOLTA PHASE PLATE TFS Selectris X FEI FALCON IV (4k x 4k) 4096 4096 2 17907 50.0 1 2164638 cryoSPARC 4.6.0 PHASE FLIPPING AND AMPLITUDE CORRECTION

Initial model generated from the data

2.52 FSC 0.143 CUT-OFF cryoSPARC 4.6.0 27750 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_63405.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 640 640 640 0 0 0 640 640 640 465.28 465.28 465.28 90.0 90.0 90.0 X Y Z -0.08748231 0.23182137 -0.00005252088 0.0062412624 0.727 0.727 0.727 0.04 AUTHOR ::::EMDATABANK.org::::EMD-63405:::: FLEXIBLE FIT REAL emd_63405_msk_1.map emd_63405_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 640 640 640 0 0 0 640 640 640 465.28 465.28 465.28 90.0 90.0 90.0 X Y Z -0.0000057903035 42.418906999999997 0.23451953 1.3957257 0.727 0.727 0.727 AUTHOR ::::EMDATABANK.org::::EMD-63405:::: emd_63405_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 640 640 640 0 0 0 640 640 640 465.28 465.28 465.28 90.0 90.0 90.0 X Y Z -0.49693984 0.50803316 0.00013900147 0.05253248 0.727 0.727 0.727 AUTHOR ::::EMDATABANK.org::::EMD-63405:::: emd_63405_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 640 640 640 0 0 0 640 640 640 465.28 465.28 465.28 90.0 90.0 90.0 X Y Z -0.3896328 0.4357169 0.00014218225 0.052396074 0.727 0.727 0.727 AUTHOR ::::EMDATABANK.org::::EMD-63405::::