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 _pdbx_modification_feature.ref_pcm_id DATA_COLLECTION em_admin _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update PDBj PDBj 2021-08-01 2022-09-21 2022-09-21 2026-09-23 Not funded Cryo-EM structure of cyanobacterial photosystem I in the presence of ferredoxin and cytochrome c6 Li J Kurisu G Photosystem I, Ferredoxin, Cytochrome c6, PHOTOSYNTHESIS Li J Hamaoka N Makino F Kawamoto A Lin Y Rogner M Nowaczyk MM Lee YH Namba K Gerle C Kurisu G Structure of cyanobacterial photosystem I complexed with ferredoxin at 1.97 angstrom resolution. Commun Biol UK 5 951 951 2022 36097054 doi:10.1038/s42003-022-03926-4 2399-3642 7fix FULLOVERLAP EMDB EMD-31605 associated EM volume
Cryo-EM structure of cyanobacterial photosystem I in the presence of ferredoxin and cytochrome c6
 Cryo-EM map of cyanobacterial photosystem I in the presence of ferredoxin and cytochrome c6 Cryo-EM map of cyanobacterial photosystem I in the presence of ferredoxin and cytochrome c6 0 1 2 3 4 5 6 7 8 9 10 11 12 13
Cytochrome C6 was not be built in model because of limited resolution
Thermosynechococcus elongatus BP-1 1.08 Photosystem I trimer 1 1 2 3 4 5 7 8 9 10 11
12 subunits with 10x his-tag on N-ter of PsaF in each monomer.
 Ga-Substituted Ferredoxin 1 6 12 13 Thermosynechococcus elongatus BP-1 Photosystem I P700 chlorophyll a apoprotein A1 Thermosynechococcus vestitus BP-1 BP-1 0.083267773 3 LEVO MTISPPEREPKVRVVVDNDPVPTSFEKWAKPGHFDRTLARGPQTTTWIWNLHALAHDFDTHTSDLEDISRKIFSAHFGHL AVVFIWLSGMYFHGAKFSNYEAWLADPTGIKPSAQVVWPIVGQGILNGDVGGGFHGIQITSGLFQLWRASGITNEFQLYC TAIGGLVMAGLMLFAGWFHYHKRAPKLEWFQNVESMLNHHLAGLLGLGSLAWAGHQIHVSLPINKLLDAGVAAKDIPLPH EFILNPSLMAELYPKVDWGFFSGVIPFFTFNWAAYSDFLTFNGGLNPVTGGLWLSDTAHHHLAIAVLFIIAGHMYRTNWG IGHSLKEILEAHKGPFTGAGHKGLYEVLTTSWHAQLAINLAMMGSLSIIVAQHMYAMPPYPYLATDYPTQLSLFTHHMWI GGFLVVGGAAHGAIFMVRDYDPAMNQNNVLDRVLRHRDAIISHLNWVCIFLGFHSFGLYVHNDTMRAFGRPQDMFSDTGI QLQPVFAQWVQNLHTLAPGGTAPNAAATASVAFGGDVVAVGGKVAMMPIVLGTADFMVHHIHAFTIHVTVLILLKGVLFA RSSRLIPDKANLGFRFPCDGPGRGGTCQVSGWDHVFLGLFWMYNCISVVIFHFSWKMQSDVWGTVAPDGTVSHITGGNFA QSAITINGWLRDFLWAQASQVIGSYGSALSAYGLLFLGAHFIWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPAIQPR ALSIIQGRAVGVAHYLLGGIATTWAFFLARIISVG P0A405 1.97.1.12 Photosystem I P700 chlorophyll a apoprotein A2 Thermosynechococcus vestitus BP-1 BP-1 0.083123648 3 LEVO MATKFPKFSQDLAQDPTTRRIWYAIAMAHDFESHDGMTEENLYQKIFASHFGHLAIIFLWVSGSLFHVAWQGNFEQWVQD PVNTRPIAHAIWDPQFGKAAVDAFTQAGASNPVDIAYSGVYHWWYTIGMRTNGDLYQGAIFLLILASLALFAGWLHLQPK FRPSLSWFKNAESRLNHHLAGLFGVSSLAWAGHLIHVAIPESRGQHVGWDNFLSTMPHPAGLAPFFTGNWGVYAQNPDTA SHVFGTAQGAGTAILTFLGGFHPQTESLWLTDMAHHHLAIAVLFIVAGHMYRTQFGIGHSIKEMMDAKDFFGTKVEGPFN MPHQGIYETYNNSLHFQLGWHLACLGVITSLVAQHMYSLPPYAFIAQDHTTMAALYTHHQYIAGFLMVGAFAHGAIFLVR DYDPAQNKGNVLDRVLQHKEAIISHLSWVSLFLGFHTLGLYVHNDVVVAFGTPEKQILIEPVFAQFIQAAHGKLLYGFDT LLSNPDSIASTAWPNYGNVWLPGWLDAINSGTNSLFLTIGPGDFLVHHAIALGLHTTTLILVKGALDARGSKLMPDKKDF GYAFPCDGPGRGGTCDISAWDAFYLAMFWMLNTIGWVTFYWHWKHLGVWEGNVAQFNESSTYLMGWLRDYLWLNSSQLIN GYNPFGTNNLSVWAWMFLFGHLVWATGFMFLISWRGYWQELIETLVWAHERTPLANLVRWKDKPVALSIVQARLVGLAHF SVGYILTYAAFLIASTAAKFG P0A407 1.97.1.12 Photosystem I iron-sulfur center Thermosynechococcus vestitus BP-1 BP-1 0.008809207 3 LEVO MAHTVKIYDTCIGCTQCVRACPTDVLEMVPWDGCKAGQIASSPRTEDCVGCKRCETACPTDFLSIRVYLGAETTRSMGLA Y P0A415 1.97.1.12 Photosystem I reaction center subunit II Thermosynechococcus vestitus BP-1 BP-1 0.015389494 3 LEVO MTTLTGQPPLYGGSTGGLLSAADTEEKYAITWTSPKEQVFEMPTAGAAVMREGENLVYFARKEQCLALAAQQLRPRKIND YKIYRIFPDGETVLIHPKDGVFPEKVNKGREAVNSVPRSIGQNPNPSQLKFTGKKPYDP P0A420 Photosystem I reaction center subunit IV Thermosynechococcus vestitus BP-1 BP-1 0.008399485 3 LEVO MVQRGSKVKILRPESYWYNEVGTVASVDQTPGVKYPVIVRFDKVNYTGYSGSASGVNTNNFALHEVQEVAPPKKGK P0A423 Photosystem I reaction center subunit III Thermosynechococcus vestitus BP-1 BP-1 0.019098062000000002 3 Thermosynechococcus vestitus BP-1 LEVO HHHHHHHHHHMRRFLALLLVLTLWLGFTPLASADVAGLVPCKDSPAFQKRAAAAVNTTADPASGQKRFERYSQALCGEDG LPHLVVDGRLSRAGDFLIPSVLFLYIAGWIGWVGRAYLIAVRNSGEANEKEIIIDVPLAIKCMLTGFAWPLAALKELASG ELTAKDNEITVSPR P0A401 Photosystem I reaction center subunit VIII Thermosynechococcus vestitus BP-1 BP-1 0.0042972340000000005 3 LEVO MMGSYAASFLPWIFIPVVCWLMPTVVMGLLFLYIEGEA P0A427 Photosystem I reaction center subunit IX Thermosynechococcus vestitus BP-1 BP-1 0.004770698 3 LEVO MKHFLTYLSTAPVLAAIWMTITAGILIEFNRFYPDLLFHPL P0A429 Photosystem I reaction center subunit PsaK Thermosynechococcus vestitus BP-1 BP-1 0.008483983 3 LEVO MVLATLPDTTWTPSVGLVVILCNLFAIALGRYAIQSRGKGPGLPIALPALFEGFGLPELLATTSFGHLLAAGVVSGLQYA GAL P0A425 Photosystem I reaction center subunit XI Thermosynechococcus vestitus BP-1 BP-1 0.016261684999999998 3 LEVO MAEELVKPYNGDPFVGHLSTPISDSGLVKTFIGNLPAYRQGLSPILRGLEVGMAHGYFLIGPWVKLGPLRDSDVANLGGL ISGIALILVATACLAAYGLVSFQKGGSSSDPLKTSEGWSQFTAGFFVGAMGSAFVAFFLLENFSVVDGIMTGLFN Q8DGB4 Photosystem I reaction center subunit XII Thermosynechococcus vestitus BP-1 BP-1 0.0034261149999999995 3 LEVO MALTDTQVYVALVIALLPAVLAFRLSTELYK P0A403 Ferredoxin-1 Thermosynechococcus vestitus BP-1 BP-1 0.010853959 3 Escherichia coli LEVO MATYKVTLVRPDGSETTIDVPEDEYILDVAEEQGLDLPFSCRAGACSTCAGKLLEGEVDQSDQSFLDDDQIEKGFVLTCV AYPRSDCKILTNQEEELY P0A3C9 Photosystem I 4.8K protein Thermosynechococcus vestitus BP-1 BP-1 0.004424317 3 Thermosynechococcus vestitus BP-1 LEVO MSTMATKSAKPTYAFRTFWAVLLLAINFLVAAYYFGILK Q8DKP6 CHLOROPHYLL A ISOMER 0.000893489 3 CL0 CHLOROPHYLL A 0.000893489 285 CLA PHYLLOQUINONE 0.000450696 6 PQN IRON/SULFUR CLUSTER 0.00035163999999999996 9 SF4 BETA-CAROTENE 0.000536873 72 BCR 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 9 LHG UNKNOWN LIGAND 4.0078e-05 51 UNL DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 3 DGD CALCIUM ION 4.0078e-05 3 CA [2Ga-2S] cluster 0.000203576 3 GAK water 1.8015e-05 348 HOH singleParticle particle 30 8.0 Quantifoil R1.2/1.3 COPPER 300 GLOW DISCHARGE ETHANE 100 277 FEI VITROBOT MARK IV JEOL CRYO ARM 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.5 1.5 NITROGEN GATAN K3 BIOQUANTUM (6k x 4k) 48.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION C3 1.97 FSC 0.143 CUT-OFF 207142 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_31605.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 322.4 322.4 322.4 90.0 90.0 90.0 X Y Z -0.024400305 0.089562714 -0.00020721252 0.002811805 0.806 0.806 0.806 0.007 AUTHOR 3D refined map in C3 symmetry, which was used for model building and refinement. emd_31605_msk_1.map emd_31605_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 322.4 322.4 322.4 90.0 90.0 90.0 X Y Z -0.09074801 0.2978233 -0.000061685394 0.007230708 0.806 0.806 0.806 AUTHOR Post-process map in C1 symmetry. (Resolution: 2.08 A) emd_31605_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 322.4 322.4 322.4 90.0 90.0 90.0 X Y Z -0.19513643 0.47528785 -0.00020721798 0.011565029 0.806 0.806 0.806 AUTHOR Post-process map in C3 symmetry. (Resolution: 1.97 A) emd_31605_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 322.4 322.4 322.4 90.0 90.0 90.0 X Y Z -0.027943557 0.10523882 -0.00020785641 0.0032609599 0.806 0.806 0.806 AUTHOR Half map of 3D refine. emd_31605_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 322.4 322.4 322.4 90.0 90.0 90.0 X Y Z -0.026756302 0.104683034 -0.00020657953 0.0032595994 0.806 0.806 0.806 AUTHOR Half map of 3D refine.