2026-08-12 REL PDBc INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond em_admin pdbx_entry_details pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order pdbx_struct_conn_angle pdbx_validate_chiral struct_conn _chem_comp_atom.pdbx_stereo_config _em_admin.last_update _pdbx_entry_details.has_protein_modification EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update PDBj PDBc 2023-09-08 2024-06-05 2024-06-05 2026-08-12 Chinese Academy of Sciences YSBR-004 China Li XY Mao ZY Shen JR Han GY Photosystem II, PHOTOSYNTHESIS Mao Z Li X Li Z Shen L Li X Yang Y Wang W Kuang T Shen JR Han G Nat Commun UK 15 4535 4535 2024 38806516 doi:10.1038/s41467-024-48878-x 2041-1723 8wb4 FULLOVERLAP EMDB EMD-37414 associated EM volume

Structure of PSII-ACPII supercomplex from cryptophyte algae

Structure of PSII-ACPII supercomplex from cryptophyte algae Structure of PSII-ACPII supercomplex from cryptophyte algae 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 Chroomonas placoidea Photosystem II reaction center M Chroomonas placoidea 0.011880879

Author stated: We did not find the sequence of chain m,M in the transcriptome of Chroomonas placoidea, so the sequence in Guillardia theta (strain CCMP2712) (tax id 905079) was used.

2 LEVO MQRLALLVAATIASAAAFAPTPALTGLRQQAPLCSGNKLSAACRAPRAAKPAMTMSLAETTNQAMLLAEGGMNVSVAAYL AVLLGTFIPVVFLLTLYIQSESRKAAETGSEGDKF L1IFP3 ACPII-1 Chroomonas placoidea 0.025151223 2 LEVO KMLRLSILAACLAAAQAFTSPAALLRPSTRAAVSRGPSMQLYKDGIIQGLGVEAIPGAGRPANLDGTLVGDVGFDPLGFS NWLDLRWAREAEIKHGRVAMLAATGMIVQDAYKFPGFEGEFGGAAMMKLHNLAVEQGAMQQLLLWLGLLEIISGVPAIIQ TLNGSERQPGDFGFDPLNCGANPDTLARRQLTELKNGRLAMIAVGGMVHHYLLVGRGPIEFITNIPNFKNPLPPF ACPII-2 Chroomonas placoidea 0.023471201 2 LEVO AMLRVALIAAILASASAFAPMGSLGLVKSARSGAAISPRMQSGDFSAAVPFLKRPSNLDGTLAGDVGFDPLGFSDVFDLR VLREAELKHGRFAMLAVLGFLVQEVYTFPFFPKMAPVDAHDYFVTQGGGSQIIFWISFVEIFGVVALFELIQGKRDAGDF AFDPLGLGKDEATLARYKVAEIKHARLAMIAIGGFIHQFWVTKQTVLEQLGNFQSLA ACPII-3 Chroomonas placoidea 0.02405502 2 LEVO ITHSRMLRTAILALCVAGASAFTASPALYKSASRKAAVSGMKMQDRSYAMPFLSRPPALDGSMAGDVGFDPLGFSNYFDL KWLREAELKHGRVCMLGCLGFLVQEQANLPLPGFDNKLATEAFFSVPAGGLWQIFFSLGAIEIITNKGKLTPGSMFTGGR APGDLDFDPLNLSVDETALRRFELAELKHARLAMIGLGGMLHQMLLTKQAPIEQLTNFKSLA ACPII-4 Chroomonas placoidea 0.023734623 2 LEVO AVVLAACVASAAAFAPGASVLPRAAARATSTKGPSMQLLPLYGEGKLQGPGTQAIPGSEPPPALDGTWVGDVGFDPLGFS RVIDMRWLREAELKHGRVCMLAATGMIVQDIALFPGVTKTFGPAKITALHDVAVKQGSMQQLLVWLGFLEIFGFVAIVQM LQGSGRQPGDFGFDPLNCGANTDTLARRQLVELKNGRLAMIATGGMIHHFFLTGKGPIEFITTLGA ACPII-5 Chroomonas placoidea 0.023762241999999996 2 LEVO ACASAAAFAPGAMPSIGKAPRAVSKTAPRMAVFPGQFSDSVPFLKQPTNLDGSYVGDVGFDPLGFSDVFDIRVLREAELK HGRIAMLATLGMVVQEAYTFPFFDKVLPIPAHDVIVKSGGMSQILLWTSFAEIFGGIALFQTIQGKRAPGDYSFDPLNLS ANDLEKRERYALAEIKHSRLAMLAFSGMVHQYFITNQGVIEQINNFRPINGFPDATFS ACPII-6 Chroomonas placoidea 0.023923800999999998 2 LEVO PAMFRAALLLACLASASAFAPGSLMMPKSATRAAISRGPRMQANDDLAVPFLERPPMLDGSYAGDIGFDPVGFSNYFDLR WLREAELKHGRVCMLGVVGFLVQEFVTLPMFSNGVTPVDDFFVVPATGLWQIFFTIGFVEAFSNGFKLTPSDMFADDRAP GDLGFDPLGCGKDPAALARRQLVEVKNGRLAMIAFGGMLHQQLLTKQGVIEQLTNFKAIM Photosystem II protein D1 Chroomonas placoidea 0.03959091 2 LEVO MTATLERRESASAWERFCSWITSTDNRLYIGWFGVLMIPTLLTATTVYIIAFVAAPPVDIDGIREPVAGSLLYGNNIITG AVIPSSASIGIHFYPIWEAASLDEWLYNGGPYQLIVDHFLLGVCGWIGREWEFSYRLGMRPWISVAFTAPVAAASAVFLV YPIGQGSFSDGMPLGISGTFNFMLVFQAEHNILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESANYGYKFG QEEETYNIVAAHGYFGRLIFQYASFNNSRALHFFLGLWPVVGIWFTALGVMTMAFNLNGFNFNQSVVDSQGRVINTWADI LNRANLGMEVMHERNAHNFPLDLAAGESLPVALTAPAVNG A0A222AI41 1.10.3.9 Photosystem II D2 protein Chroomonas placoidea 0.039216812 2 LEVO MTIAIGQEEGRGWFDLIDDWLKRDRFVFVGWSGLLLFPTSYLSIGGWFTGTTFVTSWYTHGLASSYLEGCNFFTAAVSTP ANSMGHSLLLLWGPEAQGDFTRWCQIGGLWAFCALHGSFALIGFCLRQFEIARLVGIRPYNAIAFSGPIAIFVSVFLMYP LGQASWFFAPSLGVAAIFRFLLFIQGFHNFTLNPFHMMGVAGILGAALLCAIHGATVQNTIFEDGDAANTFRAFTPTQAE ETYSMVTANRFWSQIFGVAFSNKRWLHFFMLFVPLAGLWTSAIGIVGLALNLRAYDFVSQELRAAEDPEFETFYTKNILL NEGIRSWMAAQDQPHENFIFPEEVLPRGNAL A0A222AI37 1.10.3.9 Cytochrome b559 subunit alpha Chroomonas placoidea 0.009505692999999999 2 LEVO MSGGSTGERPFSDIITSIRYWIIHSITIPALYVAGWLFVSTGLAYDIFGTPRPNEYFTQDRQQVPLVNDRFSAKQELEDL TKGL A0A222AI74 Cytochrome b559 subunit beta Chroomonas placoidea 0.004845769 2 LEVO MSKIQQPVSYPIFTFRWLAIHGLAVPTVFFLGAITSMQFIQR A0A222AI51 Photosystem II reaction center protein H Chroomonas placoidea 0.007519886999999999 2 LEVO MALRTRLGELLRPLNSEYGKVAPGWGTTPIMGFVMLLFFLFLLIILQIYNSSLIIENVDVDWASLGS A0A222AIE4 Photosystem II reaction center protein I Chroomonas placoidea 0.004424081 2 LEVO MFTLKIVVYTTVTFFVSLFTFGFLSNDASRNPNRKDLE A0A222AI80 Photosystem II reaction center protein J Chroomonas placoidea 0.003964609 2 LEVO MASTGRIPLWLIATVGGTLALTVVGIFFYGSYSGVGSSL A0A222AI54 Photosystem II reaction center protein K Chroomonas placoidea 0.005005114 2 LEVO MEAILLIAKLPEAYAVFKPIIDVAPVIPVFFLLLAFVWQAAVGFR A0A222AIA0 Photosystem II reaction center protein O Chroomonas placoidea 0.034995546999999995 2 LEVO LAMARLAILLGLVASAAAFTGPAVLPLKASNRAAACSVTMQDNSLAKKAAGIAAIPLSFLLGVNAANAITTEDIRGLTYS QVKGTGLANRCPEVSEQNAGGTIKFADDKKYKVTELCLEPKSFQIEEEVTKRRGETKKEFVDTKLMTRATYSLTGIEGPI VFKDGGLTFLEKGGIDYAATTVQLPGGERVPFLFTIKELEGKFSSSQVSAGTELGGNFKTPSYRTGLFLDPKGRGGTTGY DMAVALPGLEADGGEGQDELFAETNKVFQVTDGSIEMAFNRVDGTNGEFSGVFVSEQLSDTDMGSKAPKKVLLKGIVFGK IEEQTGDEDY Photosystem II reaction center protein Q Chroomonas placoidea 0.001805216 2 LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) Photosystem II reaction center protein R Chroomonas placoidea 0.002230741 2 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) CCPII-S Chroomonas placoidea 0.030531848 2 LEVO DHKRSRMMKSLALAAVGLAVGAEAFAPTPMVGGAKLALRTSSTRSVATVGPKMAMDVNAIVEGAQYLTAAVPNVPFVDEI TGEPQGLTAPIVHFGSVISLWLLFALPVWSAAYKAAGADTAEWVGVSQVTEDAPGIGLYGKYAPEYDGPTFREGLEYVLS FAWKPPILIAWKPRADLDRAMMDPARDTVVSSLYKSLGGALDKTAVYDEEDQLLILSDMETFPETELGRRRVAQAEAAGW FTGNPSFGKSLIEYSEETKKGMREPGTVSISAKELAALRAEAAKK Photosystem II reaction center protein T Chroomonas placoidea 0.003664447 2 LEVO METLVYVFLLAGTLGVIFFAVFFRDPPRIAKK A0A222AID2 Photosystem II reaction center protein U Chroomonas placoidea 0.015962294 2 LEVO LIAALAVSASAFSPAVPALRTAPQACGITMQAESVDRRGFLGALGAAVVAAPLAASANVEYPNVPYLGGSDIIDVNNANV RVYTRLPGMYPAIAKKIIKRAPYKDINEMLEKGDFTAAEKDILDKYLPNLTALEPAPEYVIDNINNGLYR Photosystem II cytochrome c550 Chroomonas placoidea 0.017708234 2 LEVO MLKRFSSLNIILGMLLVSFVASPVHATDLDENTRTVPLDSSGTTVILTPEQVKRGKRLFNSSCGNCHVGGITKTNPNLGL EPDALSLATPARDNIDALVDYMKNPTTYDGLESIAELHPSVKSADIFPKMRSLSDEDLFAIGGHILLQPKLSSEKWGGGK IYY A0A222AI35 Photosystem II reaction center X protein Chroomonas placoidea 0.004149939 2 LEVO MTPSLSAFINSLLLGLFVVVIPIGAALFLVSQSDRVTRT A0A222AI61 Photosystem II reaction center protein Ycf12 Chroomonas placoidea 0.003763581 2 LEVO MFNPTTLFQLIALFLVITSGPAIIVLIAFRRGNL A0A222AI69 Photosystem II reaction center protein Z Chroomonas placoidea 0.006573989999999999 2 LEVO MVGLLQILVSILILLSFALVVGVPVILVSPGEWEKSKGLVYSAAGLWFGLVIVIAAFNSFVI A0A222AI96 Photosystem II CP47 reaction center protein Chroomonas placoidea 0.056354171999999994 2 LEVO MGLPWYRVHTVVLNDPGRLIAVHLMHTALVAGWAGSMALYELAVFDPSDPVLNPMWRQGMFVMPFMARIGVTDSWGGWSV TGESVANPGFWSFEGVALAHIGLSGLLFLAAVWHWVYWDLELFRDPRTGNPALDLPKIFGIHLLLSGVLCFGFGAFHVTG AWGPGIWVSDAYGITGKVQPVAPAWGAEGFNPFNPSGVASHHIAAGILGFLAGIFHIAVRPPQRLYRALRMGNIETVLSS SIAAVFWSAFITTGTMWYGSATTPIELFGPTRYQWDSGYFQQEIERRVENSLNEGLNLSEAWSRIPDKLAFYDYIGNNPA KGGLFRAGPMNKGDGIAEAWLGHPIFQDKEGKELTVRRMPAFFETFPVILVDKDGIIRADIPFRRAESKYSIEQVGVTVS FYGGKLNGQVFKDAPTVKKYARKAQLGEVLEFDRTTLESDGVFRSSPRGWYTFGHANFALLFFLGHLWHGSRTLFRDVFS GIGAEVTEQVEFGAFQKLGDRSTKKQGAV A0A222AIE3 Photosystem II CP43 reaction center protein Chroomonas placoidea 0.050508488 2 LEVO METPFNSSLSVAGRDIESTGFAWWSGNSRLINVSGKLLGAHVAHAGLMVFWCGAMTLFEVAHYIPEKPLYEQGLILLPHL AVLGWGVGPGGEIIDIYPYFVVGVLHLISSAVLGFGGVYHSLIGPDTLEESFPAFGYDWRDKNKITTILGIHLIVLGIGA FLLVIKAMYVGGIYDTWAPGGGDVRIIDSPTLNPGVIFGYVLKSPWGGDGWIVSVNNMEDLVGGHIWIGIICIVGGFWHI FTKPFAWARRAYVWSGEAYLSYSLVAVSLMGFIASQYSWYNNTAYPSEFYGPTGPEASQSQAFTFLVRDQRLGANVSSAQ GPTGLGKYLMRSPSGEIILGGETQRFWDLRAPWIEPLRGPNGLDLNKIKNDIQPWQERRAAEYMTHAPLGSLNSVGGVAT EINSVNYVSPRSWLTCAHFFLGFAFYIGHLWHAGRARAAAAGFEKGINRENEPTLSLRPID A0A222AI36 Photosystem II reaction center protein G Chroomonas placoidea 0.005464727999999999 2 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) Photosystem II reaction center protein L Chroomonas placoidea 0.004363087 2 LEVO MSGPNPNKQPVELNRTSLFWGLLLIFVLAVLFSSYFFN A0A222AI58 Photosystem II reaction center protein W Chroomonas placoidea 0.011994986000000001 2 LEVO SKVLFLALCLVAGASAFNAPAPMALRASKTAMTMKAEGPMPKLAKALAPAIAAANIAIASPVFAEGTGEALGIDDTRLIV PVILIPVITFILYAGFASEQDNEDFFDTYDQRRK (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene 0.000536873 24 8CT CHLOROPHYLL A 0.000893489 208 CLA Chlorophyll c2 0.000608926 12 KC2 (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol 0.00056484 42 II0 (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol 0.000566856 4 II3 (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol 0.000550856 10 IHT 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 20 LMG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 18 LHG 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL 0.0007951159999999999 8 SQD CA-MN4-O5 CLUSTER 0.00033982699999999996 2 OEX PHEOPHYTIN A 0.0008712 4 PHO CHLORIDE ION 3.5453e-05 2 CL 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE 0.000749201 4 PL9 BICARBONATE ION 6.1017e-05 2 BCT DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 10 DGD FE (II) ION 5.5845e-05 2 FE2 PROTOPORPHYRIN IX CONTAINING FE 0.000616487 4 HEM singleParticle particle 7.5 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 2.0 GATAN K3 BIOQUANTUM (6k x 4k) 60.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 2.47 FSC 0.143 CUT-OFF 305400 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_37414_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 532.48 532.48 532.48 90.0 90.0 90.0 X Y Z -0.4327917 1.5068864 0.0012590496 0.04383619 1.04 1.04 1.04 AUTHOR ::::EMDATABANK.org::::EMD-37414:::: emd_37414_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 532.48 532.48 532.48 90.0 90.0 90.0 X Y Z -0.4323751 1.444293 0.0012495687 0.043818593 1.04 1.04 1.04 AUTHOR ::::EMDATABANK.org::::EMD-37414::::