Trimeric photosystem I of Acaryochloris marina NIES-2412

2026-09-02 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY chem_comp chem_comp_bond em_admin pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order pdbx_struct_conn_angle pdbx_validate_close_contact struct_conn struct_conn_type _chem_comp.formula _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update PDBe PDBe 2025-09-01 2026-07-08 2026-07-08 2026-09-02 Netherlands Organisation for Scientific Research (NWO) 714.018.001 Netherlands European Research Council (ERC) 101141764 European Union UK Research and Innovation (UKRI) MR/T017546/1 United Kingdom UK Research and Innovation (UKRI) MR/T017546/2 United Kingdom UK Research and Innovation (UKRI) MR/Y011635/1 United Kingdom Biotechnology and Biological Sciences Research Council (BBSRC) BB/X019284/1 United Kingdom H2020 Marie Curie Actions of the European Commission 955520 European Union Biotechnology and Biological Sciences Research Council (BBSRC) BB/R001383/1 United Kingdom Biotechnology and Biological Sciences Research Council (BBSRC) BB/V002015/1 United Kingdom Biotechnology and Biological Sciences Research Council (BBSRC) BB/R00921X United Kingdom Biotechnology and Biological Sciences Research Council (BBSRC) BB/Z516740/1 United Kingdom Leverhulme Trust RPG-2022-203 United Kingdom Trimeric photosystem I of Acaryochloris marina NIES-2412 Leong HF Consoli G Chlorophyll d, photosystem I, ELECTRON TRANSPORT Oliver TJ Elias E Consoli G Leong HF Cordon-Preciado V Fantuzzi A Cardona T Rutherford AW Croce R Far-red chlorophyll d clusters extend photosystem I absorption toward the red limit. Sci Adv US 12 eaed7355 eaed7355 2026 42268959 doi:10.1126/sciadv.aed7355 2375-2548 Pettersen EF Goddard TD Huang CC Meng EC Couch GS Croll TI Morris JH Ferrin TE UCSF ChimeraX: Structure visualization for researchers, educators, and developers Protein Sci. US 2018 28710774 doi:10.1002/pro.3943 0961-8368 0353 PRCIEI 9sk3 FULLOVERLAP PDB-Dev pdb_00009S6P focused EM volume

wwPDB deposition of the model built using the locally refined map on one monomer out of the homotrimer

EMDB EMD-54956 associated EM volume

Trimeric PSI Trimeric PSI 0 4 5 11 12

trimeric photosystem I from A. marina NIES - 2412

Acaryochloris marina NIES-2412 0.922 Photosystem I protein PsaA Acaryochloris marina NIES-2412 0.083573766 3 LEVO MTNSPGGPETKGRTAEVDINPVKASLEVAGKPGHFNKSLSKGPQTTTWIWNLHALAHDFDTQTNDLEEISRKIFSAHFGH LAIVFVWISGMIFHAARFSNYYAWLADPLGNKPSAHVVWPIVGQDILNADVGNGFHGIQITSGLFHILRGAGMTAPIELY STSIGALVAAAVTMYAGYFHYHKKAPKLEWFQNAEATIGGHLINLLGLGNLAWTGHLIHVSLPINKMLDSGMAPEDIPIP HEYLLDKAFMADLYPSFAQGLAPYFTLNWGVYSDFLTFKGGLDPQTGGLWMTDIAHHHLALAVMYIIAGHMYRTNWGIGH HMREIMDAHKGPFTGEGHKGLYDVLTTSWHAQLAINLACWGSFSIVCAHHMYAMPPYPYLATDYATQLNLFVHHMWLGGF YIVGGAAHAAIFMVRDYDPAMNQNNVLDRMLRHRDTIIAHLNWVCLFLGFHSFDLYIHNDEMRSLGRPQDMFSDTAIQLQ PIFAQWVQNLQANVAGTIRAPLAEGATSLAWGGDPMFVGGKVAMQHVSLGTADFMIHHIHAFQIHVTVLILLKGVLYARS SRLIPDKASLGFRFPCDGPGRGGTCQSSGWDHVFLGLFWMYNCISIVNFHFFWKMQSDVWGTANASGGINYLTAGNWAQS SITINGWLRDFLWAQSVQVINSYGSALSAYGILFLGAHFIWAFSLMFLFSGRGYWQELIESIVWAHSKLKIAPAIQPRAM SITQGRAVGLGHYLLGGIVTSWSFYLARILALG Photosystem I protein PsaB Acaryochloris marina NIES-2412 0.082083172 3 LEVO MATKFPSFSQDLAQDPTTRRIWYGIATVHDFETHDGMTEENLYQKIFATHFGHLSIIFLWTAGLLFHVAWQGNFEQWIQD PLTVRPIAHAIWDPHLGDAATQAFTQAGASGPVDLCYSGVYHWWYTIGMRTNGDLYSGSIFLMVVAAVMLFAGWLHLQPK FRPSLAWFRDAESQMNHHLAVLFGASSLGWTGHLIHVAIPEARGQHVGWDNFLSTMPHPAGLAPFFTGRWAVYAQNPDTT GHIFGTSEGAGTAILTFVGGFHPQTEALWLTDIAHHHLAIAVLYIVAGHMYRTQFGIGHSMKEIMDAHRDPWYGATLEGL YDTYNESLHFQLAFHLAALGVITEVVAQHMYSLPSYAFISQDYVTQAALYTHHQYIGGFLALGAYAHGGIFFVRDYDPER NKGNALSRLLEHKEAIISHLSWVSMFLGFHTLDLYVHNDVVVAFGTPEKQILPEPIFAEWVQAAHGKLLLGLDSLLSNPQ SIAATAWPNYGDVWLPGWLDAVNGSSTPFLNIGPGDFLVHHGIAFSIHVTVLICVKGCLDARGSKLMPDKKDFGYSFPCD GPGRGGTCDISAWDSFYLATFWMLNTIGWVTFYFNWKQLSVWSGNLAQFNNDSTYLMGWLRDYLWGYSAQLINGYTPFGV NSLSVWAWIFLLGHLCWATGFLFLISWRGYWQELIETLVWAHQRTPLANLVMWKDKPVALSIVQGRLVGLVHFAVGYFVT YGAFVIGATAPLG Photosystem I protein PsaC Acaryochloris marina NIES-2412 0.008825207 3 LEVO MSHTVKIYDTCIGCTQCVRACPTDVLEMVPWDGCKAGQIASSPRTEDCVGCKRCETACPTDFLSIRVYLGAETTRSMGLA Y Photosystem I protein PsaD Acaryochloris marina NIES-2412 0.015125149999999999 3 LEVO MAETLTGQTPLFGGSTGGLLSSAETEEKYAITWTSPKQQVFEMPTGGAAVMNEGENLLYLARKEQCLALGLRQLRIKKIM DYKIYRVLPDGSNTLLHPKDGVFPEKSNEGRAAVNSVARSIGENPNPGAIKYTGKQAYD Photosystem I protein PsaE Acaryochloris marina NIES-2412 0.009350654 3 LEVO MVQRGSKVRILRPESYWFREIGTVASVDKSGIKYPVIVRFDTCNYNGISGTAAGINTNNFGVHELEEVEAPKAKAKKPAA APKAEG Photosystem I protein PsaF Acaryochloris marina NIES-2412 0.017691422 3 LEVO MRRLFAVLVVLTLWLGVVPPASADIGGLVPCSESPQFQERAAKARNTTGDPESGRKRFEMYSSALCGADDGLPRIIAGGP WSRAGDFLIPGLLFIYIAGGIGNASRNYQIANRKKNPKNPAMGEIIIDVPLALSSTIAALAWPLKALGEVTSGKLTVPDS DVTVSPR Photosystem I protein PsaI Acaryochloris marina NIES-2412 0.0036483369999999998 3 LEVO MISDILPAIMTPLVVLIGGGAAMTAFFYYVEREG Photosystem I protein PsaJ Acaryochloris marina NIES-2412 0.005457358 3 LEVO PPQIDSEKGFMKFFSTAPVIAFVFFTLTAGFLVELNRFFPDILFFPY Photosystem I protein PsaK Acaryochloris marina NIES-2412 0.008894473 3 LEVO MFTPTFLTVAVRAVNWTPTVGVVMIAANIMAIAIAKYSIQYPNVGPSMPASSLFGGFSFNAVLGTQVFGHVLGAGAILGL TYLGVL Photosystem I protein PsaL Acaryochloris marina NIES-2412 0.015588004 3 LEVO MTMEMVKHGGDPFVGDLATPVNSSGIVKAWINNLPAYRKGMSANARGLEIGMAHGYYLYGPFATSGPVRGTTMALVSGVL SASCVIIVLTVAMQLYSSLSVPKPRPSVTTADPGSDFGTKEGWSAIGSGFLIGGCGGAVIAGVLSYAIAIFAG Photosystem I protein PsaM Acaryochloris marina NIES-2412 0.003204925 3 LEVO MELSDLQIVIALVVALLPALLALNLGTALSK Photosystem I protein PsaX2 Acaryochloris marina NIES-2412 0.0029735749999999996 3 LEVO KNPWPTLPLIWSGIGILAAIWITLQIG CHLOROPHYLL D ISOMER 0.000895462 3 G9R PHEOPHYTIN A 0.0008712 6 PHO CHLOROPHYLL D 0.000895462 279 CL7 PHYLLOQUINONE 0.000450696 6 PQN (6'S)-beta,epsilon-carotene 0.000536873 57 A1JPJ 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 6 LHG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 3 LMG IRON/SULFUR CLUSTER 0.00035163999999999996 9 SF4 water 1.8015e-05 93 HOH singleParticle particle 1 6.5

50 mM MES, 1 M betaine monohydrate, 20 mM CaCl2, 5 mM MgCl2 and 10% (v/v) glycerol, pH 6.5 adjusted with NaOH

UltrAuFoil GOLD 300 PLASMA CLEANING 100 ETHANE 95 277 FEI VITROBOT MARK IV TFS KRIOS SPOT SCAN BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.8 2.0 GATAN K3 (6k x 4k) 5120 4096 40.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 2.63 FSC 0.143 CUT-OFF cryoSPARC 151833 ANGULAR RECONSTITUTION ANGULAR RECONSTITUTION emd_54956.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 634.8 634.8 634.8 90.0 90.0 90.0 X Y Z -0.4549089 1.4354782 0.000010587908 0.019938467 1.058 1.058 1.058 0.1 AUTHOR ::::EMDATABANK.org::::EMD-54956:::: emd_54956_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 634.8 634.8 634.8 90.0 90.0 90.0 X Y Z -0.61709654 1.5889938 0.00041083453 0.06943607 1.058 1.058 1.058 AUTHOR ::::EMDATABANK.org::::EMD-54956:::: emd_54956_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 634.8 634.8 634.8 90.0 90.0 90.0 X Y Z -0.59361315 1.4025575 0.00041508625 0.069578335 1.058 1.058 1.058 AUTHOR ::::EMDATABANK.org::::EMD-54956::::