2026-08-12 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 pdbx_validate_close_contact struct_conn struct_conn_type _chem_comp.formula _chem_comp_atom.pdbx_stereo_config _em_admin.last_update PDBj PDBj 2021-06-21 2022-04-06 2022-04-06 2026-08-12 Cryo-EM Structure of primitive cyanobacterium photosystem I Kato K Hamaguchi T Photosystem I, ELECTRON TRANSPORT, PHOTOSYNTHESIS Kato K Hamaguchi T Nagao R Kawakami K Ueno Y Suzuki T Uchida H Murakami A Nakajima Y Yokono M Akimoto S Dohmae N Yonekura K Shen JR Structural basis for the absence of low-energy chlorophylls responsible for photoprotection from a primitive cyanobacterial PSI Biorxiv US 2022 doi:10.1101/2021.09.29.462462 2692-8205 7f4v FULLOVERLAP EMDB EMD-31455 associated EM volume
Cryo-EM Structure of primitive cyanobacterium photosystem I
 PSI trimer PSI trimer 0 1 2 3 4 5 6 7 8 9 10 Gloeobacter violaceus PCC 7421 1.1 Photosystem I P700 chlorophyll a apoprotein A1 Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) ATCC 29082 / PCC 7421 0.086505219 3 LEVO MSTTPQEREKPVRVLVDNDPVPTSTEKWGKPGWFERNLARGPKTTTWIWDLHALAHDFETHTSDKEEISRKIFSAHFGHL AVVCVWLSGMFWHGAYFSNFTAWMENPLGLKPSAQTVWPVFGQEILNDPSTVAKGFEQGGIVITSGLFHLWRAVGFTTTG QLAAMSIAMLIIAALFLFAGWFHYHKRAPKLEWFQNVESMLNHHLAGLFGLGSLFWTGHLIHVALPVKAQLDAGIAPAQV NPFAGLDYGLMGQYFPKGFGPNGGLGAFFTLNWGQFTDFLTFKGGLEPATGALYLTDIAHHHLAIATLFIIAGHMYRTNW GIGHSIKEMLEAHKGPLTGEGHRGLYEVLTTSWHAQLAINLAMAGSITIIVAHHMYAMNPYPYMGTDYATQISLFTHHMW IGGFLIVGAGAHAAIFMVRDYDPVTNQNNLLDRVLRHRDAIISHLNWVTLFLGFHSFGLYVHNDTMQALGRPRDMFADFA IPLQPVFAQWIQNIHAAAPGGATAPWVGGTSPTWYTGALSSAATLQANQVLALANDKISISPIHLGTADFMVHHIFALCI HVTVLILLKGVLFARSSRLIPDKANLGFRFPCDGPGRGGTCQSSAWDHVFLGLFWMYNTISVVIFHFSWKMQSDVWGTVD RSTGAVNHIIGNTDVLLGGQTVALSQYAASSININGWLRDFLWAQSSAVINSYGGPLSAYGLMFLGAHFIWAFSLMFLFS GRGYWQELIESIVWAHNKLKVAPAIQPRALSITQGRAVGVAHYLLGGIATTWAFFLARFLALP Q7NFT6 1.97.1.12 Photosystem I P700 chlorophyll a apoprotein A2 Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) ATCC 29082 / PCC 7421 0.09616675799999999 3 LEVO MATRFPKFSQDLAQDPTTRRIWYGIATAHDFESHDGMTEESLYQKLFATHFGHLAIIFLWSSGNLFHIAWQGNFEQWVSN PTGVVPIAHAIWDPHFGKGAVEAFTPEGGAGPVNAAYSGLYYLYYTLGMRFNSDLYQGSIFLMVLATVFLIAGWLHLQPR FRPSLAWFKNAESRLNHHLSALFGVSSLAFAGHMIHVAIPAARGQRVDWSNFLNTLPHPAGLAPFFTGNWGVYADPQAGP PILTFIGGLNPATGTLWLTDIAHHHLAIAVIFIIAGHMYRTNFGIGHSIKEILDAHKGPLTGEGHRGLYDTINNSLHFQL GLALASLGVVTSLVAQHTYALPAYFYMPQDHTTMAALYTHHQYIAGFLMVGAFAHGAIFFVRDYDPKANENNVLARMLEH KEALISHLSWVSLFLGFHTLGLYVHNDVMLAFGRPEDQLLIEPVFAQFVQVQSGKIIEGIPALFGGPGVTAPGEFLTGWL GSVNANNSPIFLPIGPGDFLVHHAIALGLHTTTLILVKGALDARGSKLMPDKKDFGFAFPCDGPGRGGTCDISAWDAFYL AVFWMLNTIGWVTFYWHWKWISIWGDNVAQFNASSTYLMGWLRDYLWANSAPLIGGYSPSGGTNALSVWAWMFLFGHLVW ATGFMFLIAWRGYWQELIETLVWAHERTPLANLVRWKDKPVAMSIVQGRLVGLAHFTIGYILTYAAFLIASTAALYPNGP AAFTPAISAEQAKGVLSEFKAKPVPGGVMLLLPENIVFDFDKSSVKLDADPALNRVVGVIQFYGSEPVEILGHTDSLGED AYNQKLSEERASAVKAFFEKKGIEAERLTAKGYGETKPVAPNAKPDGSDNPDGRQQNRRVEILIKTEVVPVS Q7NFT5 1.97.1.12 Photosystem I iron-sulfur center Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) ATCC 29082 / PCC 7421 0.00880717 3 LEVO MSHSVKIYDTCIGCTQCVRACPLDVLEMVPWDGNKAGTIASSPRTEDCVGCKRCETACPTDFLSIRVYLGAETTRSMGLA Y Q7NG86 1.97.1.12 Photosystem I reaction center subunit II Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) ATCC 29082 / PCC 7421 0.015952242 3 LEVO MADVKELPFGGSTPLFGGSTGGLLRKAQIEEKYLIVWNSKEEQVFEMPTGGAATMVAGTNVLYLARKEQCHALHRQLVST FKIRDSKIYRVYPNGEQVLIFPMDGVPSEKSNPGREVVGYVPRKIGDNPNPVDVKFTGKETFDV Q7NF26 Photosystem I reaction center subunit IV Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) ATCC 29082 / PCC 7421 0.007468415 3 LEVO MAIERGAKVRILRKESYWYREVGTVASVDKSEKTIYPVTVRFEKVNYSGINTNNFGVSELEEVEA Q7NFW6 Photosystem I reaction center subunit III Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) ATCC 29082 / PCC 7421 0.019931127 3 LEVO MSNKQSRVPFGAALLGILTLLLLFETGAFAQTQVKDPLKLCKDVPAYQELKTQRLEAAQKAQADGKPVTFNEAGTKQKFE RYDTAYCGQDGYPHLITSGQLDRAGDFLIPSVLFLWIAGALGWAGRLYLAESKGPEDEIIIDLPKAIKCLLLGLIWPVQA IPELISGKIRVPEDRVTISPR Q7NH05 Photosystem I reaction center subunit Z Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) ATCC 29082 / PCC 7421 0.003853611 3 LEVO MQSYNVFPALVIITTLVVPFMAAAALLFIIERDPS P0C029 Unknown protein Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) ATCC 29082 / PCC 7421 0.0028264749999999997 3 LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) Photosystem I reaction center subunit XI Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) ATCC 29082 / PCC 7421 0.015806324 3 LEVO MTLARYVYTPDPQEGTLLTPVNNSTAIRWFIDNLPINRVGMDEFTRGLEIGMAHGYWLIGPFALLGPLRNTELGLVAGLV STIGLLLISTIGLSGYASLVEDVPTEFDRKGWSRLAGGFLVGGVGGAIFAFAILQFFPLVSAIARIP Q7NIE7 Photosystem I reaction center subunit XII Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) ATCC 29082 / PCC 7421 0.003212907 3 LEVO MAATVVSGAQVAIAFVVALIAGIAALLLSTALGK Q7NHY3 CHLOROPHYLL A ISOMER 0.000893489 3 CL0 CHLOROPHYLL A 0.000893489 264 CLA Menaquinone-4 0.000444648 6 1L3 IRON/SULFUR CLUSTER 0.00035163999999999996 9 SF4 BETA-CAROTENE 0.000536873 60 BCR 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 9 LHG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 3 LMG water 1.8015e-05 402 HOH singleParticle particle 1.68 6.5 20.0 MES-NaOH 0.03 DDM Quantifoil R1.2/1.3 COPPER 200 CARBON GLOW DISCHARGE ETHANE 100 277 FEI VITROBOT MARK IV JEOL CRYO ARM 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K3 (6k x 4k) COUNTING 70.22 1 CTFFIND 4.1 PHASE FLIPPING AND AMPLITUDE CORRECTION An initial model was generated de novo from 2D classification. C3 FOURIER SPACE 2.04 FSC 0.143 CUT-OFF RELION 3.1 261743 MAXIMUM LIKELIHOOD RELION 3.1 MAXIMUM LIKELIHOOD RELION 3.1 RELION 3.1 emd_31455.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 329.2 329.2 329.2 90.0 90.0 90.0 X Y Z -0.23874322 0.46545348 0.00047807692 0.008708103 0.823 0.823 0.823 0.045 AUTHOR FLEXIBLE FIT REAL