PSI-FCPI of the diatom Thalassiosira pseudonana CCMP1335

2026-08-12 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update STRUCTURE_SUMMARY chem_comp chem_comp_atom chem_comp_bond citation citation_author em_admin entity pdbx_entity_nonpoly _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp_atom.atom_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.value_order _em_admin.last_update _entity.pdbx_description _pdbx_entity_nonpoly.name 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 2023-12-26 2024-10-30 2024-10-30 2026-08-12 Not funded PSI-FCPI of the diatom Thalassiosira pseudonana CCMP1335 Kato K Nakajima Y Shen JR Nagao R Photosystem I, ELECTRON TRANSPORT, PHOTOSYNTHESIS Kato K Nakajima Y Xing J Kumazawa M Ogawa H Shen JR Ifuku K Nagao R Structural basis for molecular assembly of fucoxanthin chlorophyll a / c -binding proteins in a diatom photosystem I supercomplex. Elife US 13 2024 39480899 doi:10.7554/eLife.99858 2050-084X 8xls FULLOVERLAP EMDB EMD-38457 associated EM volume

PSI-FCPI PSI-FCPI 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 Thalassiosira pseudonana CCMP1335 0.55 Photosystem I P700 chlorophyll a apoprotein A1 Thalassiosira pseudonana CCMP1335 0.08372582799999999 1 LEVO MAISSTERRSKNVQVFVEKDAVETSFAKWAQPGHFSRTLAKGPKTTTWIWNLHADAHDFDSQTSSLEEVSRKIFSAHFGQ LAIIFLWISGMHFHGAYFSNYSAWLTDPISIKQSSQVVWPIVGQEILNADVGGNFQGIQTTSGWFQMWRAEGITSEVELY WTAIGGLAMSAIMLFAGWFHYHKAAPKLEWFQNAESMMNHHLAGLLGLGCLSWSGHQIHIALPINKLLDAGVSPQEIPLP HEFLINRDLMAQLYPSFSKGLAPFFGGNWGEYSDFLTFKGGLNPVTGGLWLSDIAHHHLALSVLFIIAGHMYRTNWGIGH NMKEILEAHKGPFTGEGHKGLYEILTTSWHAQLAINLAMMGSLSIIVAHHMYAMPPYPYLATDYATQLSLFTHHMWIGGF CVVGGAAHGAIFMVRDYTPANNYNNLLDRVLRHRDAIISHLNWVCIFLGCHAFGFYIHNDTMRALGRPQDMFSDKAIQLQ PIFAQWIQNIHLLAPGTTAPNALATTSYAFGGDVIEVGGKIAMMPIKLGTADFMVHHIHAFTIHVTVLILLKGVLYARSS KLIPDKANLGFRFPCDGPGRGGTCQSSSWDHVFLGLFWMYNSISVVIFHFSWKMQSDVWGTITPDGAISHITGGNFAQSS ITINGWLRDFLWSQASQVIQSYGSASSAYGLIFLGAHFIWAFSLMFLFSGRGYWQELIESIVWAHNKLNFAPTIQPRALS ITQGRAVGLAHYLLGGIGTTWAFFLARAISIT A0T0M8 1.97.1.12 Photosystem I P700 chlorophyll a apoprotein A2 Thalassiosira pseudonana CCMP1335 0.082173875 1 LEVO MATKFPKFSQALAQDPATRRIWYGIATAHDLEAHDGMTEENLYQKIFASHFGHLAIIFLWTSGNLFHVAWQGNFEKWVSN PLKTRPIAHSIWDPHFGESALKAFSKGNTYPVNITFSGLYQWWYTIGFRTNQELYKGSIGLLLLASVLLIAGWLHLQPKF RPSLSWFKNNESRLNHHLSGLLGFSSLAWTGHLVHVAIPASRGVHVGWDNFLTTPPHPAGLTPFFTGNWTVYAENPDSAT HVFNTSEGSGTAILTFLGGFHPQTQSLWLSDMAHHHLAIAVVFIVAGHMYRTNFGIGHNMKEILDAHRPPGGRLGAGHVG LFETITNSLHMQLGLALACLGVATSLTAQHMYALTPYAYLSKDFTTEAALYTHHQYIAGFLMVGAFAHGAIFFVRDYDPE LNKNNVLARMLEHKEAIISHLSWASLFLGFHTLGLYIHNDTVVAFGQPEKQILFEPLFAEYIQAASGKAVYQFNVLLASS TSPATAAGNQVWLPGWLEAINNPKTDLFLKIGPGDFLVHHAIALGLHVTALILVKGALDARGSKLMPDKKDFGYSFPCDG PGRGGTCDISAWDAFYLAMFWMLNTIGWVTFYWHWKHMTIWGGNPGQFDESSNYIMGWLRDYLWLNSSPLINGYNPFGMN NLSVWSWMFLFGHLIWATGFMFLISWRGYWQELIETLVWAHERTPLANLIRWRDKPVALSIVQARLVGLVHFSVGYILTY AAFVIASTSGKFA A0T0M9 1.97.1.12 Photosystem I iron-sulfur center Thalassiosira pseudonana CCMP1335 0.008807169 1 LEVO MSHTVKIYDTCIGCTQCVRACPTDVLEMVPWDGCKSGQIASSPRVEDCVGCKRCETACPTDFLSVRVYLGAETTRSLGLA Y A0T0W4 1.97.1.12 Photosystem I reaction center subunit II Thalassiosira pseudonana CCMP1335 0.015535667999999999 1 LEVO MTLNLKTPFPTFGGSTGGWLRAAEVEEKYAITWTSTKEQIFEMPTGGAAIMRNGENLLYLARKEQCLALSTQLRTFKIND YKIYRIFPSGEVQYLHPKDGVFPEKVNPGRTSVNSRGFSIGKNPNPASIKFSGITTYES A0T0T5 Photosystem I reaction center subunit IV Thalassiosira pseudonana CCMP1335 0.007520497 1 LEVO MIDRNSKVRILRKESYWFNQIGTVATVDQSGIRYPAVVRFESVNYAGTNTNNFALDELVEVKKEK A0T0P9 Photosystem I reaction center subunit III Thalassiosira pseudonana CCMP1335 0.020382460999999998 1 LEVO MKRVNLLTLLFAVLIALTPNQALAEIGGLTKCSESAAFTKRLNASVKKLEQRASQYEADSPPALALKQQVERTQARFDKY SRSELLCGADGLPHLVADGRWSHAAEFILPGFGFIYISGWIGWVGRKYLRAVSTSANPSESEIIINVPLALKIMTTGYIW PISAWQELISNDLVAVSEEITVSPR A0T0V0 Photosystem I reaction center subunit VIII Thalassiosira pseudonana CCMP1335 0.003919688 1 LEVO MAASFLPSILVPLVGLIFPAFSMALFFLYVQTDDIA A0T0S9 Photosystem I reaction center subunit IX Thalassiosira pseudonana CCMP1335 0.004854705 1 LEVO MNDFQKYLSTAPVLLTLWMTFTAGFIIEVNRFFPDMLGLYF A0T0V1 Photosystem I reaction center subunit XI Thalassiosira pseudonana CCMP1335 0.015715207 1 LEVO MANFIKPYNDDPFVGHLATPITSSSLTRALLKNLPAYRFGLTPLLRGLEIGLAHGYFLIGPFAQLGPLRNSDIGLLAGFL STIGLILILTLGLTIYGAAAFGQEKSNGSELQTKKSWDQFKGGFFVGACGSAGFAFICLSSIPTFALN A0T0U5 Photosystem I reaction center subunit XII Thalassiosira pseudonana CCMP1335 0.003271954 1 LEVO MITDFQVYIALMAALLASVLAIRLGATLYQ A0T0S1 Photosystem I reaction center subunit Psa29 Thalassiosira pseudonana CCMP1335 0.020048312000000002 1 LEVO MKIVLIALSAASVSAFAPNAFGVRRTCYFEWLDLTIPSCGETTSLNVDLDYGMKNSYVPATGGDGGQGQFGAQSPNDWRV AGTSPVGETSYAGAADGGEEPWFAEAISTVSLDLQKADETLKAFTKDAAAFKIEEFAAEKPYGFTSSDAAMEELVGKLGY SKFLEMSTKQLMKTWGTLHPDPAAAKEE B8BUW3 Unknown protein Thalassiosira pseudonana CCMP1335 0.007166824999999999 1 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)(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)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) Fucoxanthin chlorophyll a/c-binding protein RedCAP Thalassiosira pseudonana CCMP1335 0.023695039 1 LEVO MKTAALVTLALAGSAQAFAPSTSRVSVSRTSTSVASSVFDDAVKDWAEEYPQFAAWGWGPSVQAEIWNGRHAMFGWVVMC ACAYAKGHGLIPDADQTLDLKEWGTLATISGKNTITNERAIILIANVHALMVGLAATISPNSFADTLLLDPNHPMYEWQM ERNSKLGGVMPNLGKMGVTPEAELANGRMAMMGIITCIAYSGIQGQSMIDTINEWVGGAYF Fucoxanthin chl a/c light-harvesting protein Thalassiosira pseudonana CCMP1335 0.021438559 1 LEVO MLKAVLTTSLIAAASAFAPASVGRSTVALNEMSKSIPFLTVPEKLDGSMAGDVGFDPMGLSDIQTDLNYARWAELKHGRI CMLAVVGMVWQEYGPHLPGDAYATKDPWEAISSVGFASNFQTLLAIGVVELANWNKYYGDGTPGDIGWTGGQLSKMNDAQ IKTRMESEIVHCRLAMIAFIGATHQTFLLHKGLLDFSY B8C2K6 Pt17531-like protein Thalassiosira pseudonana CCMP1335 0.021210223 1 LEVO MKTAILATLAASAAAFAPASISSPSTTQLSAWRDEVVVGITAPVGFFDPLGLSKGKDDATMAYYREAELKNGRVAMAACL GWYLNAGGVHPAFNSELSNDPLKAMVELPAVGWLQFVLGCGAIEWLGQQIKERPGYVPGDLLGASYWVDNSDEGWVMYQN KELNNGRLAMLAIVGMVYQDVFVGDYGDMMYKQLVR B8CEQ3 Fucoxanthin chl a/c light-harvesting protein, major type Thalassiosira pseudonana CCMP1335 0.021502491999999998 1 LEVO MKTACLIASSLIASASAFAPAPVAKSTTALSADFSGEIGAANAELGCWDPLNFCTDQASFDKMRYAELKHGRVAQLAAWG YATTWSGARFPGCEDFPAGHEAVLKIGTENLIPVLVVAGALETLWKQKEGSFPGDFSATSFPVGFGPFAKTEADMIDLRT KELNNGRAAMMGILGMIVHEQIDGKPFIFFDKFEIYAPFGN B5YM25 Fucoxanthin chlorophyll a/c-binding protein Lhcq8 Thalassiosira pseudonana CCMP1335 0.02111209 1 LEVO MKSVCIALLASSVSAFAPSQQGPVKSALSYASELDSMTGTGIESPKVFDPLNLSDYVPVDWARRAELSNGRSAMLATVGW FFPKVFGTFDSTDVTTTDPIDAIMQADPQWWAQWILICGVFETWKYKKEMEGKSFLGGADPAVDYLKLWPADAAAQEEMK TKELKNARLAMIGIAGFAANHFIPGSCPVPDFIA B8C770 CHLOROPHYLL A ISOMER 0.000893489 1 CL0 CHLOROPHYLL A 0.000893489 138 CLA PHYLLOQUINONE 0.000450696 2 PQN IRON/SULFUR CLUSTER 0.00035163999999999996 3 SF4 BETA-CAROTENE 0.000536873 20 BCR 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 7 LHG DODECYL-BETA-D-MALTOSIDE 0.000510615 4 LMT UNKNOWN LIGAND 89 UNL DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 1 DGD Zeaxanthin 0.000568871 1 5X6 (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol 0.000582855 7 DD6 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 1 LMG Chlorophyll c1 0.000610941 7 KC1 (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate 0.0006589059999999999 15 A86 water 1.8015e-05 922 HOH singleParticle particle 3.0 6.5 20.0 MES-NaOH MES 0.03 DDM DDM Quantifoil R1.2/1.3 COPPER 300 CARBON GLOW DISCHARGE 10 ETHANE 100 277 FEI VITROBOT MARK IV JEOL CRYO ARM 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.2 1.8 60000.0 GATAN K3 (6k x 4k) COUNTING 50.0 1 2733572 CTFFIND 4.1 PHASE FLIPPING AND AMPLITUDE CORRECTION An initial model was generated de novo from 2D classification. C1 FOURIER SPACE 2.3 FSC 0.143 CUT-OFF RELION 4.0 75667 MAXIMUM LIKELIHOOD RELION 4.0 MAXIMUM LIKELIHOOD RELION 4.0 RELION 4.0 emd_38457.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 254 254 254 0 0 0 254 254 254 191.008 191.008 191.008 90.0 90.0 90.0 X Y Z -0.040055446 0.097367026 0.0005549062 0.004254923 0.752 0.752 0.752 0.012 AUTHOR ::::EMDATABANK.org::::EMD-38457:::: Other experimental model

ModelAngelo

FLEXIBLE FIT RECIPROCAL emd_38457_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 254 254 254 0 0 0 254 254 254 191.008 191.008 191.008 90.0 90.0 90.0 X Y Z -0.024207784 0.07631893 0.0006081149 0.003494318 0.752 0.752 0.752 AUTHOR ::::EMDATABANK.org::::EMD-38457:::: emd_38457_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 254 254 254 0 0 0 254 254 254 191.008 191.008 191.008 90.0 90.0 90.0 X Y Z -0.031492054 0.06505326 0.00049937225 0.005223949 0.752 0.752 0.752 AUTHOR ::::EMDATABANK.org::::EMD-38457:::: emd_38457_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 254 254 254 0 0 0 254 254 254 191.008 191.008 191.008 90.0 90.0 90.0 X Y Z -0.027809998 0.059104912 0.00049865874 0.005200603 0.752 0.752 0.752 AUTHOR ::::EMDATABANK.org::::EMD-38457::::