Cryo-EM structure of PSI-11ACPIs from Rhodomonas sp. NIES-2332 at 2.14 angstrom resolution

2025-12-31 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 PDBj PDBj 2024-12-12 2025-11-26 2025-11-26 2025-12-31 Japan Society for the Promotion of Science (JSPS) JP22H04916 Japan Cryo-EM structure of PSI-11ACPIs from Rhodomonas sp. NIES-2332 at 2.14 angstrom resolution Zhang WY 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 9l0k FULLOVERLAP EMDB EMD-62717 associated EM volume

Photosystem I complex binding with 11 ACPIs Photosystem I complex binding with 11 ACPIs 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 Rhodomonas sp. NIES-2332 0.726968 Photosystem I P700 chlorophyll a apoprotein A1 Rhodomonas sp. NIES-2332 0.08344160899999999 1 LEVO MTISSKEQEAKKVSITVDRDPVATSFEKWAQPGHFSRTLAKGPKTTTWIWNLHADVHDFDSHTNSLEDISRKIFSAHFGQ LSIIFLWLSGMYFHGARFSNYSAWLSNPTAVKPSAQVVWPIVGQEILNGDVGGGFQGVQVTSGFFQIWRASGITSEVELY WCALAGLLMSGLMIFAGWFHYHKAAPKLEWFQNAESMLNHHLSGLLGLGCLSWAGHQIHISLPVNKLLDAGVAPQEIPLP HEFLVNRDLMAQLYPSFSKGLVPFFTLNWSEYSDFLTFKGGLNPVTGGLWLSDTAHHHLALAVLFIVAGHMYRTNWGIGH SMKEILEAHKGPFTGEGHKGLYEILTTSWHAQLAINLAMMGSVSIIVAHHMYAMPPYPYIATDYPTQLSIFTHHMWIGGF CVVGGAAHAGIFMVRDYNPAQNYNNLLDRVIRHRDAIISHLNWICIFLGFHSFGLYIHNDTMRALGRTQDMFSDTAIQLK PVFAQWVQSIHTLAPGNTTPNALATASYAFGGDVVAVGNKVAMMPISLGTADFMVHHIHAFTIHVTVLILLKGVLFSRNS RLIPDKANLGFRFPCDGPGRGGTCQSSAWDSVFLGLFWMYNCISVVIFHFSWKMQSDVWGTVQADGTVTHITGGNFAQSA ITINGWLRDFLWAQASQVIQSYGSALSAYGLIFLGAHFIWAFSLMFLFSGRGYWQELIESIVWAHNKLNVAPAIQPRALS ITQGRAVGLAHYLLGGIGTTWAFFLARIISVG Photosystem I P700 chlorophyll a apoprotein A2 Rhodomonas sp. NIES-2332 0.082087664 1 LEVO MATKFPKFSQALAQDPATRRIWYGLATAHDLESHDGMTEENLYQKIFASHFGHLAVIFLWTSGNLFHLAWQGNFEQWVLN PLKVKPIAHAIWDPHFGQPAVKAFTKGGVSYPVNIATSGVYHWWYTIGMRSNTDLYAGSLFLLFLAGVFLFAGWLHLQPK FRPGLSWFKNNESRLNHHLSGLFGFSSLAWSAHLIHVAIPEARGQHVGWDNFTKVAPHPAGLQPFFSGNWGVYAAAPDTT NHIFGTSEGAGTAILTFLGGFHPQTQALWLTDIAHHHLAIGVVFIFAGHMYRTNWGIGHSLKEILDAHRPPGGRLGAGHK GIFETLTNSLHFQLGLALASLGVITSLVAQHMYALPSYAFIAKDYVTQSALYTHHQYIAGFLMVGAFAHGAIFFVRDYDP EQNKNNVLARILDHKEAIISHLSWVSLFLGFHTLGIYVHNDVVVAFGTPEKQILVEPVFAQWIQASSGKALYGFDVFLSS SNSVATNASSNIWLPGWLEAINSGKNSLFLPIGPGDFLIHHAIALALHTTTLILVKGALDARGSKLMPDKKDFGYSFPCD GPGRGGTCDISAWDAFYLSMFWMLNTIGWVTFYWHWKHVTIWQGNAGQFNESSTYIMGWLRDYLWLNSSPLINGYNPFGM NSLSVWSWMFLFGHLIWATGFMFLISWRGYWQELIETLVWAHERTPLANLVRWKDKPVALSIVQARLVGLIHFTAGYIFT YAAFVIASTTGKFG Photosystem I iron-sulfur center Rhodomonas sp. NIES-2332 0.008759131 1 LEVO MSHSVKVYDTCIGCTQCVRACPCDVLEMVSWDGCKAGQIASAPRTEDCIGCKRCETACPTDFLSVRVYLGGETTRSMGLA Y Photosystem I reaction center subunit II Rhodomonas sp. NIES-2332 0.015585723999999999 1 LEVO MAETLNLQIPSPTFEGSTGGWLRAAEVEEKYAITWTSPKEQVFEMPTGGAAIMRQGENLLYLARKEQCLALATQVKNSFK ITDYKVYRIFPSGEVQYLHPKDGVFPEKVNAGRVGVGNVSHSIGKNLNPAQIKFTSKSFNG Photosystem I reaction center subunit IV Rhodomonas sp. NIES-2332 0.007309363 1 LEVO MVKRGSKVRILRKESYWYQDIGTVATIDTSGIRYPVVVRFEKVSYSGVNTNNFSLDEVVEVVAK Photosystem I reaction center subunit III Rhodomonas sp. NIES-2332 0.020849226999999998 1 LEVO MEIFFVKNWVSMLLVCSFLAFPSLAKADVAGLTPCGESKEFARRLDGSVKKLQTRLKKYEAGTPPALALQKQIDKTKNRF DRYGKAGLLCGTDGLPHLIADGRWSHSGEFVIPGLFFLYVAGWIGWVGRSYVLFARTADKPTEKEIIIDVPVALSFVSTG FIWPFSAFKEFTSGNLIVPADEITVSPR Photosystem I reaction center subunit VIII Rhodomonas sp. NIES-2332 0.003927708 1 LEVO MTAAYLPSILVPIIGLIFPGLVMAFAFIYIEQDEVA Photosystem I reaction center subunit IX Rhodomonas sp. NIES-2332 0.0049748119999999995 1 LEVO MDSNFLKYLSTAPVLFTVWLSFTASFIIEANRFFPDMLYFPM Photosystem I reaction center subunit XI Rhodomonas sp. NIES-2332 0.016489076000000002 1 LEVO MSQFIKPYNDDPFVGNLATPVSTSSFTKSLLSNLPAYRAGLSPLLRGVEIGLTHGYFLVGPFYKLGPLRNSDVALLSGFF SALGLIIILVACLTIYGVVSFEETEAKDQLQTAKGWRQFTSGWLVGSVGGASFAYILISNIPFLQTAGMSMLK Photosystem I reaction center subunit XII Rhodomonas sp. NIES-2332 0.0033180700000000002 1 LEVO MISDTQIFIALILALVSLVLAIRLGRALYQ Photosystem I reaction center subunit PsaK Rhodomonas sp. NIES-2332 0.008715256 1 LEVO MNADLLIALVPQTVAWSAKTGAVMVLSNILCIVAGRYVIQVKGTGPSLPISGSFAGFGLPELLASTSLGHIVGSGAILGL SYVGVLS ACPI-s Rhodomonas sp. NIES-2332 0.031529 1 LEVO LTIAFSLTMRTSVLILAGVAVAQAFSPAVVSTGGLTSVRMAQAPPPASGKPLPKAKINCLEVNKKQWGIEGGAAAPGSAA PPAPKKAAVKKAAAAAGGAAVGFSGVPSQFGRPESGVYPAEPSEQTFLGMRGPRAPGHRENFGGKHTATMLAIAALLWQP VSEAGMYRMQGDGSLTKTSFNEFEVPGFGNAKKVPTIESLFPFSSKGFDASPVLFGKNSMIVVEDPRDGCGAYANSGSCH TFLDEIGDALKASPETLPRSEGKATYSFPWMYEHVRGRSRLAVSQLGATQSLSLWVSPVRVW ACPI-c Rhodomonas sp. NIES-2332 0.023785516 1 LEVO MLRTALIAACVASASAFAPGFAPMAMKSRSSAVSSMRMQEGDFSAAVPFLKRPTNLDGQYIGDVGFDPLGFSDVFDLRVL REAELKHGRFAMLATLGFIVQELYTFPFFPKMAPVDAHDYFVKQGGGSQIIFWISFVELFGVVALFETLQGKREPGDFAF DPLGLAKDEATLERYRLAEVKHARLAMIAIGGFIHQYWVTKQTVLEQLGNFKSLA ACPI-a Rhodomonas sp. NIES-2332 0.023380866999999996 1 LEVO MMRAVLVLATGVASASAFAPAANFAGLSTSSRAAIARGPRMQEMSEAIPFLPKPANIDASMPGYSGFDPLGFSDYYNVKW MQEAEIKHGRICMLAALGMMFPEFGTLPQFSSFSTNPLEAFYQVGPAGWGQILLFIGVLESFSYEKVFYGDSAPGDLGFD PLRMSSNAASAKHYARAEVMNGRLAMIGFSGMLHHAILTKQGPITQIVEQNFVPGAR ACPI-b Rhodomonas sp. NIES-2332 0.024814875 1 LEVO MLRNVLIAACVAGTAAFTASPALFRAGAVTRATSGISGMQMQAKSKAVPFLSQPEALDGSMAGDVGFDPFGFSSNFDLKW LREAELKHGRICMLAATGCLVQEVVHLPGEAFSQKMALNAWAAAPRGGMISILVAIGLIELISNRFALTATDMFANPNRV PGDLGFDPLSLGGNGANRARMELAEITHGRAAMMGFSGMVHQMLVSKQAPIEQLMHFKAVDSSMMKLGGAAGNLGY ACPI-h Rhodomonas sp. NIES-2332 0.023646421999999997 1 LEVO SMLRSAVALALVAGATAFAPGAMGPGLQLRAQGAAQRAPARAGLSSLSMAQNPMSKAVADFAESSPEFGGRGLGVTVNAE RWNGRHAMFGIFAMVMTSYMKGHGLIPDADKILDVAQWGSLASVWDGAGNGISNERAIILIAHVHVLVVSVIAAVAPFGF QDTLVKEKGYTPEAPAGLIPPFKTGLTPEAELINGRLAMLGIISIVTASVFTGTPVVDTINLGMGKILY ACPI-m Rhodomonas sp. NIES-2332 0.022379063999999997 2 LEVO TVAAVACVASAAAFAPSAPMGVKASTRAVSKIGPRMQAMSDSVPFLKQPEALDGSMAGDVGFDPLGFSSIGDINFLREAE LKHGRIAMLAAAGSIAQDIFTFPGVSKVVGTAKMTGVHDILVKQGAMGQLLLWLSFLEVFGTIALLETLDGKRAPGDFKF DPLNFSKNPETFKRYQLAEIKNGRLAMMGVGGMVHGYFITGKGPLELLGNFK ACPI-l Rhodomonas sp. NIES-2332 0.018985741999999996 1 LEVO DNAMPFLEGPPKLDGSLAGDVGFDPVGFSNYFDIRWLREAELKHGRVCMLGVTGLLVQEAICLPQFANGKTPVDDFFVVP AAGLWQVFFTIGAVEFFSNGFKLTPGDMFSEGREAGDLGFDPLGCGKNPDALARRRLVEVKNGRLAMIAFGGMLHQQLLT GQGTLEQLANFKAIN ACPI-k Rhodomonas sp. NIES-2332 0.024658832 1 LEVO AASAFAPAALPSMARTTARSGVTMQLYKDGVMQGKGLVAVPFALAPDSLPADIPGYVGFDPLGLSTLCNLDFLREAEIKH GRVAMLAVTGSLVQDVFQFPGVDKVIGNAKMIGAHDKFIAGAHAGDTRSFAMHQIIFWVGLLEVLTMPALFETMNGGPRQ PGDFKFDPLGLGKGDKLARKQLTEIKNGRLAMIGVGGMVHHYLLTGKGPLQFLAGIPNYKSCIDPHMGPLCQ ACPI-i Rhodomonas sp. NIES-2332 0.021402548999999996 1 LEVO LLQGSGRTAAVSGLSGMKMQDMSASVPFLPRPAALDGSMVGDVGFDPLGFTTKYDIKWLREAELKHGRVCMLASLGCIVQ EFVHLPSEATSNPVASEAFFQVPAGGLWQIFAAIGIIEHFSNNFKMSGSTMFSDGRAPGDLSFDPLNFGKNPSARARYEL AEIKNGRLAMMGFSGMIHGCFITGKGPLGALGSLDWHQSF ACPI-d Rhodomonas sp. NIES-2332 0.023069039 1 LEVO LPPAMFRLSLCAAIVASASAFAPSSVLPTATRRAGAVSAMKMQMPVAIPPLGRPETDMFDGSVPGDAGFDPLVISGWLDS RWLREAEVKHGRVAMLAAAGCIAQDLFTFPGVTQVFSPGTKMSALHDAAVKAGSMQQMLWPIAILETISIAATIQMLQGS GRAPGDFGFDPLGLGKGAKAERMALCEIKNGRLAMIGFSGMMHHYFITGKGPIELLTSR PsaR Rhodomonas sp. NIES-2332 0.013949041999999998 1 LEVO SFAMAALRCTVLLLAVASASAFVSGPATLALRSNPRAAISRGPQMYSPVPSPEGTKEVYWETKAPSSDVLGIGAGVSSGN FAASSVVALMIGGFCTGQVIPLTSDPNPLFLIGSFLLPYSWALHVAAWIQKNNGK ACPI-n Rhodomonas sp. NIES-2332 0.02306983 1 LEVO LRSVAVCACLASAAAFAPSAVLPRAATRAAALRGPSMQLYKDGKMQGKGVNIIPVFARPDSLDGTIPGDQGFDPFGFSSW VNMKFVSEAEIKHGRLAMLAFAGIMVESIGISFPGATSILGDSKDIFEIHNKAVESGAMGQILLWVGFIEACVGVPAMNE MLSGETSRMPGDFGFDPLGLGKGDKLARKQLVEVTNGRLAMLAVSGIVHHTIITGKGPLQ PsaQ Rhodomonas sp. NIES-2332 0.023676062 1 LEVO YVALAAASAEAFSSPALSGLKMSAEPTQISRKDLLSTAAAGIIAVPAIAGAASLDPKTGFPVQSGGRDTLCGGSASAGCQ PMTQAASITDKQKTVLAGKITVAANKVPVLTAAVEKMKSGKKPKMDRDYVLRFSALYLTTLVDAMDQYCLRDANGAKAAG GAGIPKVGGFKSTLAPSSASALYGNVDSIKEDMQTIRDAAFKGDFDGVIKAAGDIQTSATAFLGQANPPIVFN CHLOROPHYLL A ISOMER 0.000893489 1 CL0 CHLOROPHYLL A 0.000893489 218 CLA PHYLLOQUINONE 0.000450696 2 PQN 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 18 LHG 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 28 WVN DODECYL-ALPHA-D-MALTOSIDE 0.000510615 5 LMU IRON/SULFUR CLUSTER 0.00035163999999999996 3 SF4 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL 0.0007951159999999999 1 SQD DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 2 DGD 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 8 LMG (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 45 II0 Chlorophyll c2 0.000608926 15 KC2 (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-05 411 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 8WM6 2.14 FSC 0.143 CUT-OFF 33179 NOT APPLICABLE NOT APPLICABLE emd_62717.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 -0.14326389 0.3631105 0.00006482735 0.009539852 0.727 0.727 0.727 0.032 AUTHOR ::::EMDATABANK.org::::EMD-62717:::: emd_62717_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 -0.5604654 0.8818957 0.00019214505 0.077716865 0.727 0.727 0.727 AUTHOR ::::EMDATABANK.org::::EMD-62717:::: emd_62717_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 -0.65857357 0.84899366 0.00018879936 0.07761853 0.727 0.727 0.727 AUTHOR ::::EMDATABANK.org::::EMD-62717::::