cryo-EM structure of PSII-ACPII from Rhodomonas sp. NIES-2332

2026-08-12 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.name _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.name _em_admin.last_update REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY chem_comp_atom em_admin pdbx_entry_details 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_atom.pdbx_stereo_config _em_admin.last_update _pdbx_entry_details.has_protein_modification EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update PDBj PDBj 2024-12-23 2025-11-26 2025-11-26 2026-08-12 Japan Society for the Promotion of Science (JSPS) JP22H04916 Japan cryo-EM structure of PSII-ACPII from Rhodomonas sp. NIES-2332 Yonehara N Akita F Shen JR photosynthesis complex, PHOTOSYNTHESIS Zhang W Yonehara N Ishii M Jiang H La Rocca R Tsai PC Li H Kato K Akita F Shen JR Structural analysis of PSI-ACPI and PSII-ACPII supercomplexes from a cryptophyte alga Rhodomonas sp. NIES-2332. Front Plant Sci CH 16 1716939 1716939 2025 41393888 doi:10.3389/fpls.2025.1716939 1664-462X 9l5v FULLOVERLAP EMDB EMD-62846 associated EM volume

cryo-EM struture of PSII-ACPII from Rhodomonas sp. NIES-2332

cryo-EM structure of PSII-ACPII from Rhodomonas sp. NIES-2332 cryo-EM structure of PSII-ACPII from Rhodomonas sp. NIES-2332 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 18 19 20 21 22 Rhodomonas sp. NIES-2332 Photosystem II protein D1 Rhodomonas sp. NIES-2332 0.041541246 2 LEVO TSTIVAWEVIYYNLYKNKKMTATLERRESASLWERFCSWITSTENRLYIGWFGVLMIPTLLTATTVYIIAFIAAPPVDID GIREPVAGSLLYGNNIISGAVIPSSASIGIHFYPIWEAASLDEWLYNGGPYQLIVDHFLLGVCGWIGREWEFSYRLGMRP WISVAFTAPVAAASAVFLVYPIGQGSFSDGMPLGISGTFNFMLVFQAEHNILMHPFHQLGVAGVFGGSLFSAMHGSLVTS SLIRETTENESANYGYKFGQEEETYNIVAAHGYFGRLIFQYASFNNSRALHFFLGLWPVVGIWFTALGIMTMAFNLNGFN FNQSVVDSQGRVINTWADILNRANLGMEVMHERNAHNFPLDLAAGESLPVALTA Photosystem II CP47 reaction center protein Rhodomonas sp. NIES-2332 0.056199855 2 LEVO GLPWYRVHTVVLNDPGRLIAVHLMHTALVAGWAGSMALYELAVFDPSDPVLNPMWRQGMFVMPFMARIGVTDSWGGWSIT GESVANPGFWSFEGVALAHIGLSGLLFLAAVWHWVYWDLELFRDPRTGNPALDLPKIFGIHLLLSGVLCFGFGAFHVTGA WGPGIWVSDAYGITGKVQPVAPAWGPEGFNPFNPSGVASHHIAAGILGFAAGIFHIAVRPPQRLYRALRMGNIETVLSSS IAAVFWSAFITTGTMWYGSATTPIELFGPTRYQWDSGYFQQEIERRVENSLNEGLSLSEAWSRIPDKLAFYDYVGNNPAK GGLFRAGPMNKGDGIAEAWLGHPIFQDKEGRELTVRRMPAFFETFPVILVDKDGIIRADIPFRRAESKYSIEQVGVTTSF YGGKLNGQVFTDAPTVKKYARKAQLGEVMEFDRTTLESDGVFRSSPRGWYTFGHANFALLFFLGHLWHGSRTLFRDVFSG IGAEVTEQVEFGAFQKLGDRSTKKQGAV Photosystem II CP43 reaction center protein Rhodomonas sp. NIES-2332 0.053468285000000004 2 LEVO MKVFALGWLLKISLMKTLYSLRRFYHVETPFNSNIGIAGRDIESTGFAWWSGNSRLINVSGKLLGAHVAHAGLMVFWCGA MTLFEVAHYIPEKPLYEQGLILLPHLASLGWGVGPGGEIVDIYPYFVVGILHIISSAVLGFGGVYHSLIGPDTLEESFPA FGYDWRDKNKITTILGIHLVILGFGALLLVVKAMYLGGLYDTWAPGGGDVRIIDNPTLNPAVIIGYVLKSPWGGDGWICS VNNMEDIVGGHIWIGFTCIAGGFWHILTKPFAWARRAYVWSGEAYLSYSLVAVSLMGFIASQYSWYNNTAYPSEFYGPTG PEASQSQAFTFLVRDQRLGASVASAQGPTGLGKYLMRSPSGEIILGGETQRFWDLRAPWIEPLRGPNGLDLNKIKNDIQP WQERRAAEYMTHAPLGSLNSVGGVATEINSVNFVSPRSWLTCAHFLLGFVFYIGHLWHAGRARAAAAGFEKGINRENEPV LSLRPI Photosystem II D2 protein Rhodomonas sp. NIES-2332 0.039160707 2 LEVO MTIAIGQEEGRGWFDLADDWLKRDRFVFVGWSGLLLFPTSYLSIGGWFTGTTFVTSWYTHGLASSYLEGCNFFTAAVSTP ANSMGHSLLLLWGPEAQGDFTRWCQIGGLWAFCALHGSFGLIGFCLRQFEIARLVGIRPYNAIAFSGPIAIFVSVFLMYP LGQASWFFAPSLGVAAIFRFLLFIQGFHNFTLNPFHMMGVAGILGAALLCAIHGATVQNTIFEDGDAANTFRAFTPTQAE ETYSMVTANRFWSQIFGVAFSNKRWLHFFMLFVPLAGLWTSAIGIVGLALNLRAYDFVSQELRAAEDPEFETFYTKNILL NEGIRSWMAAQDQPHENFIFPEEVLPRGNAL Cytochrome b559 subunit alpha Rhodomonas sp. NIES-2332 0.009503719999999998 2 LEVO MSGGSTGERPFSDIITSIRYWIIHSITIPALFVAGWLFVSTGLAYDIFGTPRPNEYFTQERQQVPLVNDRFSAKQELEDL TKGL Cytochrome b559 subunit beta Rhodomonas sp. NIES-2332 0.004860847 2 LEVO MSKIKQPISYPIFTFRWLAIHGLAVPTVFFLGAITSMQFIQR Photosystem II reaction center protein H Rhodomonas sp. NIES-2332 0.007429764 2 LEVO MALRTRLGELLRPLNSEYGKVAPGWGTTPIMGFVMLLFAVFLLIILQIYNSSLIIENVDVDWASLGS A6MW35 Photosystem II reaction center protein I Rhodomonas sp. NIES-2332 0.004390064999999999 2 LEVO MFTLKIVVYTTVTLFVSLFTFGFLSNDASRNPNRKDLE Photosystem II reaction center protein K Rhodomonas sp. NIES-2332 0.005025104 2 LEVO MEGIFLLAKLPEAYAVFKPIIDVAPVIPVFFLLLAFVWQAAVGFR Photosystem II reaction center protein L Rhodomonas sp. NIES-2332 0.004363087 2 LEVO MSGPNPNKQPVELNRTSLFWGLLLIFVLAVLFSSYFFN Photosystem II protein M Rhodomonas sp. NIES-2332 0.011851809999999999 2 LEVO TPFAMHASSAALLVLACAAGAAAFAPSTPALTGLKTTAFCQGPKLSAACRTPRAAKATAPSMSLMETANQAVLLAEGGMN VSVAAYLAVLLGTFVPVVFLITLFIQSEARKAAESGTE Photosystem II reaction center protein T Rhodomonas sp. NIES-2332 0.0037085 2 LEVO METLVYTFLLIGTLGVLFFAVFFRDPPRIAKK Photosystem II protein W Rhodomonas sp. NIES-2332 0.012592550999999999 2 LEVO DLIMLRTAVLCALIATAAAFSAAPMSGLQLRSGKTAMTMKSEGPMAAMNANVAKALAPAVAAFSVAAPAFAEGTGEALGV DDGRLLVPLVLIPVFVALLYGNFASTQDNEDFFDTYDQRRK Photosystem II reaction center X protein Rhodomonas sp. NIES-2332 0.004192965 2 LEVO MTPSFSAFINSLLAGLFIVIIPIGTALLIVSQSDRLTRN Photosystem II reaction center protein Psb30 Rhodomonas sp. NIES-2332 0.003662478 2 LEVO MPNLQTVAQLISLFLILTSGPAIIVLIALRRGNL Photosystem II reaction center protein Z Rhodomonas sp. NIES-2332 0.006656092 2 LEVO MVAILQLLVSMLILLSFALVVSVPVILVSPGEWEKSKGLVYTGAGLWFGLVIMTAAFNSFVI ACPII-1 Rhodomonas sp. NIES-2332 0.025355333999999997 2 LEVO MLRSAVLATVAVSASAFTSPALFTRTSTRPAVSTAPTMQLYREGVLQGLGTDAIPGTDRPKNLDGALVGDVGFDPLGFSN WLDLRWAREAEIKHGRVAMLAATGMIVQDVYKFPGVQKTFGDASMMKLHNVAVDQGAMQQLFLWITVLETLTGIPAIIQT LNGSERQPGDFGFDPLGCGRNPETLARRQLVELKNGRLAMIAVGGMVHHYLLVGRGPIEFVKNIPNFKNPLPPF ACPII-2 Rhodomonas sp. NIES-2332 0.023785516 2 LEVO MLRTALIAACVASASAFAPGFAPMAMKSRSSAVSSMRMQEGDFSAAVPFLKRPTNLDGQYIGDVGFDPLGFSDVFDLRVL REAELKHGRFAMLATLGFIVQELYTFPFFPKMAPVDAHDYFVKQGGGSQIIFWISFVELFGVVALFETLQGKREPGDFAF DPLGLAKDEATLERYRLAEVKHARLAMIAIGGFIHQYWVTKQTVLEQLGNFKSLA ACPII-3 Rhodomonas sp. NIES-2332 0.01990092 2 LEVO DRSYSMPFLERPPALDGSLAGDVGFDPLGFSNYFDLKWLREAELKHGRVCMLGCTGFITQEKIQLPLPGFDNKVATEAFF SVPAGGLWQIFFTLGAIEILSNGGKLAPGDMFADGRAPGDLGFDPLNLSGDDAALRRFILAELKHCRLAMIGLGGMLHQM LITKQGPLDQLANFQPIQYYGL ACPII-4 Rhodomonas sp. NIES-2332 0.021802331999999997 2 LEVO LPRTANRAAAKTSPTMQLYKEGVLQGITVNAIPKSERPFGLDGTYVGDVGFDPLGFSSIIDMRWLREAELKHGRVCMLAA TGMIVQDVYQFPGVTKSFGDAKMTTLHDVAVKQGSMQQLLVWLGLLEIFGFVAIVQMLQGSDRQPGDFGFDPLNCAANPD TLARRQLVELKNGRLAMIATAGMLHHFFITGKGPIQLITG ACPII-5 Rhodomonas sp. NIES-2332 0.024844620999999997 2 LEVO MFRTTLALAAVAGAAAFAPAPAFAPKASIRAATNTAPRMAVFQGDFSESVPFLKTPTNLDGSLPGDVGFDPLGFSEVFDI RVLREAELKHGRIAMLATLGYLVQEAYVFPFFDKVPPIQAHDVLVKSGGMSQILLWTSFLEIFGGIALFQTIQGRRYPGD FAFDPLGLSQGKNAEKLERYQLAEIKHSRLAMLAFSGFVHQGFITKQGVLEQLGNFKPIPGFPEATFF ACPII-6 Rhodomonas sp. NIES-2332 0.018970796999999998 2 LEVO NAMPFLERPPKLDGSLAGDVGFDPVGFSNYFDIRWLREAELKHGRVCMLGVTGLLVQEAICLPQFANGKTPVDDFFVVPA AGLWQVFFTIGAVEFFSNGFKLTPGDMFSEGREAGDLGFDPLGCGKNPDALARRRLVEVKNGRLAMIAFGGMLHQQLLTG QGTLEQLANFKAIN Psb-gama_linker Rhodomonas sp. NIES-2332 0.031784143 1 LEVO LTTRIMARTVAVLACSLLLFAPSSHAFAPAGVARVGMPLRSNAVSARSARVTPAKMAMDPSQISHIADGAQTFLSTLDTV PFIDEVTGEAQGFTAPKNHFASVIGLWVLFALPVWSAAYKQAGASNPEWFGVSQVSEDAPGIGLLAKAAPEYNGPSFREG LEYVFSFVWKPPILIAWKPRTVYDRDAMDPARDTVVSKLYKGLGGALDKTAVYDEEDQLLILSDLVTFEETDLGRRREKI AEQAGWYTGNPSFGRSLIEYSEQTRKGKKDMGTVTISTEELAKLRAEAAKKE Psb-gama_linker Rhodomonas sp. NIES-2332 0.031815221 1 LEVO LTTRIMARTVAVLACSLLLFAPSSHAFAPAGVARVGMPLRSNAVSARSARVTPAKMAMDPSQISHIADGAQTFLSTLDTV PFIDEVTGEPQGFTSPKNHFASVIGLWVLFALPVWSAAYKQAGCTTPDWFGVSQVAEDAPGVGLLAKAAPEYNGPSFREG LEYVFSFVWKPPILIAWKPRTVYDRDAMDPARDTVVSKLYKGLGGALDKTAVYDEEDQLLILSDLVTFEETDLGRRREKI AEQAGWYTGNPSFGRSLIEYSEQTRKGKKDMGTVTISTEELAKLRAEAAKKE FE (II) ION 5.5845e-05 2 FE2 CHLOROPHYLL A 0.000893489 194 CLA PHEOPHYTIN A 0.0008712 4 PHO 1,3,3-trimethyl-2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-3,7,12,16-tetramethyl-18-[(1R)-2,6,6-trimethylcyclohex-2-en-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohexene 0.000536873 24 WVN 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 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL 0.0007951159999999999 4 SQD CHLORIDE ION 3.5453e-05 3 CL MANGANESE (II) ION 5.4938e-05 4 MN 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 22 LMG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 18 LHG DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 4 DGD BICARBONATE ION 6.1017e-05 2 BCT PROTOPORPHYRIN IX CONTAINING FE 0.000616487 2 HEM Chlorophyll c2 0.000608926 22 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 46 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-(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 8 IHT water 1.8015e-05 676 HOH singleParticle particle 6.5 ETHANE TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.2 1.0 FEI FALCON IV (4k x 4k) 50.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 8XLP 2.17 FSC 0.143 CUT-OFF 28657 NOT APPLICABLE NOT APPLICABLE emd_62846.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 436.2 436.2 436.2 90.0 90.0 90.0 X Y Z -0.11587708 0.303005 0.00010152556 0.007810836 0.727 0.727 0.727 0.04 AUTHOR ::::EMDATABANK.org::::EMD-62846:::: emd_62846_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 436.2 436.2 436.2 90.0 90.0 90.0 X Y Z -0.37328643 0.57516634 0.0002127929 0.05002965 0.727 0.727 0.727 AUTHOR ::::EMDATABANK.org::::EMD-62846:::: emd_62846_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 436.2 436.2 436.2 90.0 90.0 90.0 X Y Z -0.33020255 0.5414011 0.00021423672 0.050070867 0.727 0.727 0.727 AUTHOR ::::EMDATABANK.org::::EMD-62846::::