2026-09-23 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 REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY chem_comp em_admin pdbx_modification_feature pdbx_nonpoly_atom_coordination _chem_comp.formula _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update STRUCTURE_SUMMARY em_admin pdbx_modification_feature _em_admin.last_update _pdbx_modification_feature.ref_pcm_id EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update DATA_COLLECTION em_admin _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update PDBj PDBj 2025-09-02 2026-06-17 2026-06-17 2026-09-23 Japan Society for the Promotion of Science (JSPS) 23H04958 Japan Japan Society for the Promotion of Science (JSPS) 23H04960 Japan PSI complex of A.thaliana isolated using DOC based Clear-Native-PAGE method Kawamoto A Seki S Kurisu G Photosystem I complex, membrane protein, PHOTOSYNTHESIS Yang Z Kameo S Seki S Kurisu G Tanaka R Kawamoto A Takabayashi A A novel method for cryo-EM protein sample preparation based on Clear-Native-PAGE To Be Published 0353 Liebschner D Afonine PV Baker ML Bunkoczi G Chen VB Croll TI Hintze B Hung LW Jain S McCoy AJ Moriarty NW Oeffner RD Poon BK Prisant MG Read RJ Richardson JS Richardson DC Sammito MD Sobolev OV Stockwell DH Terwilliger TC Urzhumtsev AG Videau LL Williams CJ Adams PD Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Acta Crystallogr D Struct Biol DK 75 861 877 2019 31588918 doi:10.1107/S2059798319011471 0907-4449 0353 ABCRE6 9wls FULLOVERLAP EMDB EMD-66073 associated EM volume
PSI complex of A.thaliana isolated using DOC based Clear-Native-PAGE method
 PSI complex of A.thaliana isolated DOC based Clear-Native-PAGE method PSI complex of A.thaliana isolated DOC based Clear-Native-PAGE method 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 Arabidopsis thaliana Chlorophyll a-b binding protein 6, chloroplastic Arabidopsis thaliana 0.026021895 1 LEVO MASNSLMSCGIAAVYPSLLSSSKSKFVSAGVPLPNAGNVGRIRMAAHWMPGEPRPAYLDGSAPGDFGFDPLGLGEVPANL ERYKESELIHCRWAMLAVPGILVPEALGYGNWVKAQEWAALPGGQATYLGNPVPWGTLPTILAIEFLAIAFVEHQRSMEK DPEKKKYPGGAFDPLGYSKDPKKLEELKVKEIKNGRLALLAFVGFCVQQSAYPGTGPLENLATHLADPWHNNIGDIVIPF N Q01667 Photosystem I chlorophyll a/b-binding protein 2, chloroplastic Arabidopsis thaliana 0.027782813999999996 1 LEVO MASSLCASSAIAAISSPSFLGGKKLRLKKKLTVPAVSRPDASVRAVAADPDRPIWFPGSTPPEWLDGSLPGDFGFDPLGL SSDPDSLKWNVQAEIVHCRWAMLGAAGIFIPEFLTKIGILNTPSWYTAGEQEYFTDKTTLFVVELILIGWAEGRRWADII KPGSVNTDPVFPNNKLTGTDVGYPGGLWFDPLGWGSGSPAKLKELRTKEIKNGRLAMLAVMGAWFQHIYTGTGPIDNLFA HLADPGHATIFAAFTPK Q9SYW8 Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic Arabidopsis thaliana 0.029206311 1 LEVO MAAQALVSSSLTSSVQTARQIFGSKPVASASQKKSSFVVKAAATPPVKQGANRPLWFASSQSLSYLDGSLPGDYGFDPLG LSDPEGTGGFIEPRWLAYGEIINGRFAMLGAAGAIAPEILGKAGLIPAETALPWFQTGVIPPAGTYTYWADNYTLFVLEM ALMGFAEHRRLQDWYNPGSMGKQYFLGLEKGLAGSGNPAYPGGPFFNPLGFGKDEKSLKELKLKEVKNGRLAMLAILGYF IQGLVTGVGPYQNLLDHLADPVNNNVLTSLKFH Q9SY97 Chlorophyll a-b binding protein 4, chloroplastic Arabidopsis thaliana 0.027760460999999997 1 LEVO MATVTTHASASIFRPCTSKPRFLTGSSGRLNRDLSFTSIGSSAKTSSFKVEAKKGEWLPGLASPDYLTGSLAGDNGFDPL GLAEDPENLKWFVQAELVNGRWAMLGVAGMLLPEVFTKIGIINVPEWYDAGKEQYFASSSTLFVIEFILFHYVEIRRWQD IKNPGSVNQDPIFKQYSLPKGEVGYPGGIFNPLNFAPTQEAKEKELANGRLAMLAFLGFVVQHNVTGKGPFENLLQHLSD PWHNTIVQTFN P27521 Photosystem I P700 chlorophyll a apoprotein A1 Arabidopsis thaliana 0.083315367 1 LEVO MIIRSPEPEVKILVDRDPIKTSFEEWAKPGHFSRTIAKGPDTTTWIWNLHADAHDFDSHTSDLEEISRKVFSAHFGQLSI IFLWLSGMYFHGARFSNYEAWLSDPTHIGPSAQVVWPIVGQEILNGDVGGGFRGIQITSGFFQIWRASGITSELQLYCTA IGALVFAALMLFAGWFHYHKAAPKLAWFQDVESMLNHHLAGLLGLGSLSWAGHQVHVSLPINQFLNAGVDPKEIPLPHEF ILNRDLLAQLYPSFAEGATPFFTLNWSKYSEFLTFRGGLDPVTGGLWLTDIAHHHLAIAILFLIAGHMYRTNWGIGHGIK DILEAHKGPFTGQGHKGLYEILTTSWHAQLSLNLAMLGSLTIIVAHHMYSMPPYPYLATDYATQLSLFTHHMWIGGFLIV GAAAHAAIFMVRDYDPTNRYNDLLDRVLRHRDAIISHLNWVCIFLGFHSFGLYIHNDTMSALGRPQDMFSDTAIQLQPVF AQWIQNTHALAPGVTAPGETASTSLTWGGGELVAVGGKVALLPIPLGTADFLVHHIHAFTIHVTVLILLKGVLFARSSRL IPDKANLGFRFPCDGPGRGGTCQVSAWDHVFLGLFWMYNAISVVIFHFSWKMQSDVWGSISDQGVVTHITGGNFAQSSIT INGWLRDFLWAQASQVIQSYGSSLSAYGLFFLGAHFVWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPATQPRALSII QGRAVGVTHYLLGGIATTWAFFLARIIAVG P56766 1.97.1.12 Photosystem I P700 chlorophyll a apoprotein A2 Arabidopsis thaliana 0.082555883 1 LEVO MALRFPRFSQGLAQDPTTRRIWFGIATAHDFESHDDITEERLYQNIFASHFGQLAIIFLWTSGNLFHVAWQGNFETWVQD PLHVRPIAHAIWDPHFGQPAVEAFTRGGALGPVNIAYSGVYQWWYTIGLRTNEDLYTGALFLLFLSALSLIGGWLHLQPK WKPRVSWFKNAESRLNHHLSGLFGVSSLAWTGHLVHVAIPASRGEYVRWNNFLNVLPHPQGLGPLFTGQWNLYAQNPDSS SHLFGTSQGSGTAILTLLGGFHPQTQSLWLTDMAHHHLAIAILFLIAGHMYRTNFGIGHSIKDLLEAHIPPGGRLGRGHK GLYDTINNSIHFQLGLALASLGVITSLVAQHMYSLPAYAFIAQDFTTQAALYTHHQYIAGFIMTGAFAHGAIFFIRDYNP EQNEDNVLARMLDHKEAIISHLSWASLFLGFHTLGLYVHNDVMLAFGTPEKQILIEPIFAQWIQSAHGKTSYGFDVLLSS TSGPAFNAGRSIWLPGWLNAINENSNSLFLTIGPGDFLVHHAIALGLHTTTLILVKGALDARGSKLMPDKKDFGYSFPCD GPGRGGTCDISAWDAFYLAVFWMLNTIGWVTFYWHWKHITLWQGNVSQFNESSTYLMGWLRDYLWLNSSQLINGYNPFGM NSLSVWAWMFLFGHLVWATGFMFLISWRGYWQELIETLAWAHERTPLANLIRWKDKPVALSIVQARLVGLAHFSVGYIFT YAAFLIASTSGKFG P56767 1.97.1.12 Photosystem I iron-sulfur center Arabidopsis thaliana 0.009049508999999999 1 LEVO MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWDGCKAKQIASAPRTEDCVGCKRCESACPTDFLSVRVYLWHETTRSMGLA Y P62090 1.97.1.12 Photosystem I reaction center subunit II-2, chloroplastic Arabidopsis thaliana 0.022336598 1 LEVO MATQAAGIFSPAITTTTSAVKKLHLFSSSHRPKSLSFTKTAIRAEKTESSSAAPAVKEAPVGFTPPQLDPNTPSPIFAGS TGGLLRKAQVEEFYVITWNSPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKITYQFYRVFPNGEVQYL HPKDGVYPEKANPGREGVGLNMRSIGKNVSPIEVKFTGKQSYDL Q9SA56 Photosystem I reaction center subunit IV A, chloroplastic Arabidopsis thaliana 0.014984955 1 LEVO MAMTTASTVFVLPANVTSVAGASSSRSSVSFLPMRNAGSRLVVRAAEDPAPASSSSKDSPAAAAAPDGATATKPKPPPIG PKRGSKVKILRRESYWFKNVGSVVAVDQDPKTRYPVVVRFAKVNYANISTNNYALDEVEEVAA Q9S831 Photosystem I reaction center subunit III, chloroplastic Arabidopsis thaliana 0.024203125 1 LEVO MSLTIPANLVLNPRSNKSLTQSVPKSSARFVCSDDKSSSSTPQSMKAFSAAVALSSILLSAPMPAVADISGLTPCKDSKQ FAKREKQQIKKLESSLKLYAPESAPALALNAQIEKTKRRFDNYGKYGLLCGSDGLPHLIVNGDQRHWGEFITPGILFLYI AGWIGWVGRSYLIAISGEKKPAMKEIIIDVPLASRIIFRGFIWPVAAYREFLNGDLIAKDV Q9SHE8 Photosystem I reaction center subunit V, chloroplastic Arabidopsis thaliana 0.017103271 1 LEVO MATSASALLSPTTFSTAISHKNPNSISFHGLRPLRLGGSSSALPKLSTTGRKSSSAVVRAELSPSIVISLSTGLSLFLGR FVFFNFQRENVAKQGLPEQNGKTHFEAGDDRAKEYVSLLKSNDPIGFNIVDVLAWGSIGHIVAYYILATSSNGYDPSFFG Q9S7N7 Photosystem I reaction center subunit VI-2, chloroplastic Arabidopsis thaliana 0.015291522 1 LEVO MASFATIAAVQPSAAVKGLGGSSLAGAKLFIKPSRQSFKTKSTRAGAVVAKYGDKSVYFDLEDLGNTTGQWDVYGSDAPS PYNPLQSKFFETFAAPFTKRGLLLKFLILGGGSLLTYVSANSTGDVLPIKRGPQEPPKLGPRGKL Q9SUI6 Photosystem I reaction center subunit VIII Arabidopsis thaliana 0.004137024 1 LEVO MTTFNNLPSIFVPLVGLVFPAIAMASLFLHIQKNKIF P56768 Photosystem I reaction center subunit IX Arabidopsis thaliana 0.0050118969999999995 1 LEVO MRDLKTYLSVAPVLSTLWFGSLAGLLIEINRLFPDALTFPFFSF P56769 Photosystem I reaction center subunit psaK, chloroplastic Arabidopsis thaliana 0.013219431 1 LEVO MASTMMTTLPQFNGLRATKISAAPVQGLASVQPMRRKGNGALGAKCDFIGSSTNLIMVTSTTLMLFAGRFGLAPSANRKA TAGLRLEARDSGLQTGDPAGFTLADTLACGTVGHIIGVGVVLGLKNIGAI Q9SUI5 Photosystem I reaction center subunit XI, chloroplastic Arabidopsis thaliana 0.023070557 1 LEVO MAASASPMASQLRSSFSSASLSQRLAVPKGISGAPFGVSPTKRVSSFTVRAVKSDKTTFQVVQPINGDPFIGSLETPVTS SPLIAWYLSNLPGYRTAVNPLLRGVEVGLAHGFFLVGPFVKAGPLRNTAYAGSAGSLAAAGLVVILSMCLTIYGISSFKE GEPSIAPSLTLTGRKKQPDQLQTADGWAKFTGGFFFGGISGVTWAYFLLYVLDLPYFVK Q9SUI4 Photosystem I reaction center subunit N, chloroplastic Arabidopsis thaliana 0.018451063999999996 1 LEVO MAAMNSSVLTCSYAIAGSGSVELNQKVGLVNSSVGFGQKKQMIMPVIKAQRVVGDDVDGSNGRRSAMVFLAATLFSTAAV SASANAGVIDEYLERSKTNKELNDKKRLATSGANFARAFTVQFGSCKFPENFTGCQDLAKQKKVPFISEDIALECEGKDK YKCGSNVFWKW P49107 CHLOROPHYLL B 0.000907472 9 CHL CHLOROPHYLL A 0.000893489 117 CLA UNKNOWN LIGAND 29 UNL (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL 0.00060087 3 XAT Lutein 0.000568871 8 A1LXP 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 4 LHG BETA-CAROTENE 0.000536873 23 BCR 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 6 LMG IRON/SULFUR CLUSTER 0.00035163999999999996 3 SF4 CHLOROPHYLL A ISOMER 0.000893489 1 CL0 PHYLLOQUINONE 0.000450696 2 PQN DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 1 DGD water 1.8015e-05 480 HOH singleParticle particle 7.5 25.0 Bis-Tris Bis(2-hydroxyethyl)iminotris(hydroxymethyl)methane 0.05 DDM n-Dodecyl-a-D-maltoside
25mM Bis-Tris, 0.05% a-DDM
 Quantifoil R1.2/1.3 COPPER 200 CARBON CONTINUOUS 5.0 GLOW DISCHARGE AIR ETHANE 100 277 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 0.01 0.5 1.5 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN Microscope was modified with Cs corrector GIF Bioquantum 20 GATAN K3 (6k x 4k) 1 8764 1.651 40.0 1 1629453 CTFFIND 4.1 PHASE FLIPPING ONLY 3D initial reference created using the Ab-initio program in cryoSPARC C1 BACK PROJECTION 2.18 FSC 0.143 CUT-OFF RELION 4.0.2 148985 MAXIMUM LIKELIHOOD RELION 4.0.2 MAXIMUM LIKELIHOOD RELION 4.0.2 RELION 4.0.2 emd_66073.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 392 392 392 0 0 0 392 392 392 264.6 264.6 264.6 90.0 90.0 90.0 X Y Z -0.03905465 0.10092798 0.00024124693 0.0023128507 0.675 0.675 0.675 0.00994 AUTHOR 8J7B PDB experimental model RIGID BODY FIT UCSF ChimeraX 1.9 REAL 40.083199999999998 emd_66073_msk_1.map emd_66073_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 392 392 392 0 0 0 392 392 392 264.6 264.6 264.6 90.0 90.0 90.0 X Y Z -0.006562405 0.032844797 0.00015589039 0.0012879242 0.675 0.675 0.675 AUTHOR emd_66073_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 392 392 392 0 0 0 392 392 392 264.6 264.6 264.6 90.0 90.0 90.0 X Y Z -0.016743496 0.04382384 0.00015550504 0.0022311334 0.675 0.675 0.675 AUTHOR emd_66073_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 392 392 392 0 0 0 392 392 392 264.6 264.6 264.6 90.0 90.0 90.0 X Y Z -0.015558606 0.04635181 0.00015629982 0.0022302405 0.675 0.675 0.675 AUTHOR