2026-08-12 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY chem_comp_atom em_admin pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_struct_conn_angle pdbx_validate_chiral struct_conn _chem_comp_atom.pdbx_stereo_config _em_admin.last_update PDBj PDBj 2023-05-31 2024-05-15 2024-05-15 2026-08-12 National Science Foundation (NSF, China) China Cryo-EM structure of Symbiodinium photosystem I Zhao LS Wang N Li K Zhang YZ Liu LN Symbiodinium, Photosystem I, PHOTOSYNTHESIS Zhao LS Wang N Li K Li CY Guo JP He FY Liu GM Chen XL Gao J Liu LN Zhang YZ Architecture of symbiotic dinoflagellate photosystem I-light-harvesting supercomplex in Symbiodinium. Nat Commun UK 15 2392 2392 2024 38493166 doi:10.1038/s41467-024-46791-x 2041-1723 8jjr FULLOVERLAP EMDB EMD-36366 associated EM volume
Cryo-EM structure of Symbiodinium photosystem I
 Photosystem I of Symbiodinium Photosystem I of Symbiodinium 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 Symbiodinium sp. PCPI-7 Symbiodinium sp. 0.027129824 1 LEVO MLAYGGIVTTAVLTQEKWPFFDAVVNAVPDNKQVRAPATFCGGAAPRSVSRTACHASSSKSLPFLPKPQNLGGLAGGDAE FDPLGFSDTFDVKWLRESELKHGRVCMLATVGFVAEQYIQFPGFTPAEDALQAIYTAPPNITALLLFACGYIESSAYDGK LTMLDMFDGEGAKRAPGDLNFGKRFLPGDKAAADDLATKELSNGRLAMLAFAGMVHHNLVVKGPLFPLFPEGWAGPQGSW DLDSTAGALNSGSLGL PCPI-1 Symbiodinium sp. 0.028182101999999997 1 LEVO MARVAALALSAGGLAFVVPRSSTSTSSLRGVSVSAPAAEPTSSASWGAAAATATAALGLAAASATSATRRTARKAVGVCL PLTDKFDPLNLASTDEKLERYTQVEIKHGRVAMIAVVGYIMPEIFRFPGCESFQHGLAALESIPLEGWVQLAALVGAHEV LVKPRAGGLGTSDFGLGTELLDGIEEPELERKLTAERNNGRLAMVAIMGLMVQDGMFGEPPLSYMSKNGWWGEGVQYFVQ HLNNCQSFSGSFVDNAGVCALPSRQGRTA PCP-11 Symbiodinium sp. 0.021707046999999997 1 LEVO ATKLSEGPFIETETYPAPKEMEMSAAVPFLRYPQVLKGWVGEEKGFDPLGVTDALPVYWVREAELKHGRVCMLATVGWIA TDLGMRFPGDQFQSVQTTLEAHDKMVEAGLMAPFLGAVGTFELYSLWLFFKGWEMEVNRDAGDFFLGKQFLPKEPAKEKD MRLKELENGRLAMFAFSGIVTQAAMTGQAWPFM PCPI-6 Symbiodinium sp. 0.019572627 1 LEVO GGYKMSPAVPFLPMSPALEGIPGEEEGFDPMGFSLAIDIRWLREAELKHGRVAMLATVGWIATDLGLRVPGEPFQVSTVE AHDAMVKFGSMPQMLVWMGYAELFGFLAIVNMFEGKTDRKPGDFGLRGFYPQDAKGQYDMQVKELRNGRLAMLAYGGIVT TAVLTQEKWPFFDAVVN PCPI-5 Symbiodinium sp. 0.026752761999999996 1 LEVO MAVAAGLLALPAFVPSSLTGAQAPAAPALRGNSQGSAGAGSASVGIAGAACAVLGAAALRRGVAARKALRRELAIAYEDS GIDLLDNGKFCQGLAGADGAWGRYEFDPLGFSKKTELVPYFREAELKHGRLAMLAWVGMVVPDFVRIPGEKFSFEAVPLP IDGHDAFSGATGVNAQILFWVGILEFCCAKKVFEWNSLEVAGDYGLTKFFPSDEEGQKKMRTAELKNGRLAMLAFGGAIT QAVITRHPFPWLY PCPI-8 Symbiodinium sp. 0.030544203 1 LEVO MEVAFLTPIATNVASSVAPAHAGKAPGPPGPAGASFGLTAAFGVAAALGLASRKRVQRAAQEMATLPKHMQPVDTADYPV YKPGPSGVPKLPQLVGDWGVPLPGSYKACLTMVGPDVETACEVGKPWDPLGLSKLYDRNFDFNGNMTYPHVQWLRESELK HGRCAMLAIVGIFAQQSFHIDGYPEAPWYEALKACYDNPAGIVGFGIAQISAFAMVIEGAYFPKDSWIGQMDREPGDLGF DPLKLAKDAESMKSMQLKELKNGRLAMMAFMSCVVGHYVPGSVPGV PCPI-4 Symbiodinium sp. 0.024445182 1 LEVO MLGLAGAGAVTAASMGVSQRQRVVRRAEFAAGMAGSKLHGWGEYQFDPAGFATSYPELLGWFRESELKHGRVAMLAYVGL IVPDAFRLPFEEVQDSSLDLLSAHNKLIGPGLGEGPMWWLLLACGVIESFRFKQVGLAFESLTTENAGDLGLRMFAPSSA EGMESMKMKELKNGRLAMLAIGGALTQGVLFNAHHFPFMSALRSEKQSGIGSRSTMVGTAASMGVSQR PCPI-10 Symbiodinium sp. 0.027998846 1 LEVO MALGAAAAAYLGSSAVQAFLAPSAPSPALRGAPGTSGTSASASSSGFSATSFGATAVATAALALARRGRGLVPRAAEAEP FAGGLIGGESAFAGQDFNFDPLGLATKCEKFLPWFREAELKHGRIAMLAWVGLVAPEFVRIPGPEQCYGAKTVVEAHNAC AGDPYFPFIIDATDFYGKDGHQVGPLFQVFAFCGAVEMLTTFAKTANVSNKPGLTLANAGDYRLGANFLPEDEAKAKEMK LKELKNGRLAMLAFGGAITQATLTGNGFPWL PCPI-3 Symbiodinium sp. 0.027409289 1 LEVO MFFQDGLTGSAWGDWALYTDSPLRALTPAQESIAGTGGPFPENFWDPAGITSKKSKEEILELRAIELKHGRVAMLAVLGW FHVAAGFHIIGDLATGTYLDNNPLVSVTQLPMGGMWQTVFFIMCLEWVSTYVCPPPKSKPWDILGWSDILLEDEDNYWNQ FRKAEVQELNNGRLAMMAIVGLIVQDIFFGDFGEVKVCFSSQTCQDIGDYLPGWTGPLPPVAYDFPPLYPAPEVPYTGYQ APLKLM PCPI-9 Symbiodinium sp. 0.022091139 1 LEVO MAIIGMFFQDGLTGSAWGDWANYTDSPLRAFEGELGVQAPVGYFDPLGLSKDGDVETFRRRRESELKNGRVAMFATIGYM VPEYFKFPGYLAPSASLKFADVPNGIQAITKVPAEGWLQWVALCGCYELCVNQPVDAADPGNYGKGKLGYGNMVLGITAE SISDPEARKRGLNSELANGRLAMMAIMGLWVQDGLFGTPYGLY PCPI-13 Symbiodinium sp. 0.023286387 1 LEVO MLAIAGCGLSYQAFVQTAGSSHGAPTQALRGNASQATRTNLSSASVSAAASITGLAVLGASRARGDKVRRCAEFNGADMP GATAPLGWFDPLGLGKTEERFNKMRAAELKHGRVAMMASLGCVVQHWAKFPGFESAPAGLGALSNPAALGGMGALFLGCG VLELGFWSDEAAKEPGNFGDPANFSAEYGAYSKEFRDKEINHGRMAMMAIIGQLSAEAVTGMDAAQ PCPI-12 Symbiodinium sp. 0.021881955 1 LEVO MAIIGQLSAEAVTGMDAAQQAGLAAVARPRQIQSSSAFVGAASIAPKRLTARRAFDASQEAGVTAPLGYFDPAGFVQDEE SFLNLRRAEIKHGRVAMMAALGLLVQSLIKLPGFDSVPAGLGAQWTAPGDAGLWTVVVLCGFFETGLNQWREDPKQPGNF GDPMNLGNYTMEMRNKELNNGRIAMFAVMGIISAEIYTGNVAVAQF PCPI-2 Symbiodinium sp. 0.015403753 1 LEVO SETFRRRRISEIKNGRVAMIACMGYIAPEYFRWPGYCSPSTDLKFADIPNGIQALYKMPAEAWAQIGVFIAFLELFPMRQ EKDALPGDAPNFGRLGVPFFSSKADPEKNRRGLEAEINNGRLAMVAITGMISQNAFF PsaA Symbiodinium sp. 0.076579406 1 LEVO AIFRYVNATLWSKAGHFNKALSKGAKTTTWIWNLHASAHDFDIQQGSAGLIARKVFSSGLAHLSLVFFWLGGMHFHGAYL SNYSAWLKDPKSVAPSSHIAYSLVGQDILNSYTSQYFSGITITSGFFQLYRSEGIVTQSQLKYACAASLIATLICLSGSY LHMQLMSKFTSFYKKFQSLSQSHLIIMFGFGSVSFSAHQIHEALPINSLLDSGIWDPQLFSAITGKSTMAILLGTPSAIT GKLLNPSTGSIFLSQVAAHHLAVGIVFITLGLIKWCNLFFSRNAILSLRLAYMDYHAQLSINLAVWASLSMVAAHHLTEI PVYPYESTDYPTVLCLFVHHACLSGFFTVASGAHASIFVIRQLPTSEIRHRDPIIGHLIWVCIALGLHSFGLYCHNDTLE ALGRPEDTFCDNSIQLKPIFAKQFLGLQPGIEVLDGKIVRMTQELGTADFMVHHIHAFTIHVTLLILLKGVLYARNSRLV SDKLELGFAYPCDGPGRGGTCQISPWDHLFLAVFWMYNCLSVVIFHYFWKMQSDVWGSYVHLSQHLQLHCCSSLAHSSLT CSHYSQGDFSVNSITINGWLRNLLWSEASQVIQSYALPSICSYGFIFLAAHFVWAFSLMFLFSGRAYWQELIESILWSHH KLKIVPHIQPRALSISQGRAVGLTHYVLGGIGCTWAFIISRMLVLTT PsaB Symbiodinium sp. 0.07485771899999999 1 LEVO MSFNGRCATSRYLQVMGSIHDIESYFALDNTLSLNLQIFTAHWGHLAIILMWISGNLYHIASNANYSLWIKNPIPSMPIA HNIWDPHFTSSTSTPYSHTTTAAVLIAYSGIYNQLYTSGFSTVNQIYKATFAFSCLAVISILLAKIHIRTHSEVLHNSAT HASQIPSFFQLLYFLDVGISSINIRLNFHTGVLVGFFSIAYTGHLLDVAIPASRAPLSHTSLSYLTFFGGLKSDTASLYL TDIAHHHLAIGVIFVYIGHLYSSCSTALGTYIRDMLYTSAIYMFQIKSLHLALSLALAGCAVLTSATAQHIYSLTPYFYL SYDYVTSVTLYVHHSYIASFLAIASHAHAAITLVRDWVAPLELESSCTIARIHTHKAAIISHLSWVSLWLGFHTLAIYSH NDTNMAFGSPSKQILIEPTNAQLIQESSGKALYSFAINSLANYNKSFGSFIYPIGPGDLYVHHAIALGLHVTVLILLKGA LEARGSKLMPDKMEHSFGFSCDGPGRGGTCDISAWDCFYLAMFWMLNTNAWIDFYFHYKYLAPRQFSESSTYLESWFRDY LWFNSAPLIRAYSALGTNDLSVQAWFFLLTHLAWATGFMFLISWRGYWQELIDIILYMHLKTPILIDLWNGGVYTPLALS IVQARFIGLVHFTAGLILTYPPFIISTTS PsaC Symbiodinium sp. 0.016733236 1 LEVO MSRLLMIAACAGLAARYVPQAFVPGLAQGAAPSTPHASFAEGKSTGALAGFAAVSCAIGAGAAAVQSRAARMARRSHAVK IYDTCIGCTLCVRACPTDVLEMVPATVNAAKQVASSPRVEDCVGCKRCETACPTDFLSIRVYLQENEETQYSLGLDLADW S PsaD Symbiodinium sp. 0.032748866999999994 1 LEVO MASRGVGVAAVAVFGLATVAFVAPSSGARRLRAPVAQPAAFGASAPSGTSGLWTACSLGGVVLAVGAAVTRRAESKEIVV ESIPRPEDLLESPKFPMFEGSTGGYMSRSTRERHAITWTAKDQNKFEMPTGGFAIMNKGENLCYFRKKEQCISLGKQLRK MKIENYKIYRLKKDGTVIFMHPADGVFPEKVNKGRVQVNGRPFTIRGNPQQSELKWTKYHMKSYEADPLTTLFIKARVMA FQDIPNLFALPQPNMEEMVPVEEVGEYTKQEYTTRLMEALKRVQDDRKAKEAKSL PsaE Symbiodinium sp. 0.013089104999999998 1 LEVO MARVRSLALLLAAAYALAPCFVGSAAALDGSRLGATARSAEAKKKAKAPWVGPKKGSWVKVLRPESYWYQTRGQVVNVNQ KPEIKYPVTVKFDRVNFSNVNTNGFALWEVIEAPAPGPGEV PsaF Symbiodinium sp. 0.029733779 1 LEVO MARPGSALLCVAAATVLVAAAVAFVGSPAGTHAPSTGRSVELGSRALPPAAESAAASGEAAAEQSGAESFMKWTAAGLLA GLVMAVSSSTPASALPKPTDMFGGVDIDLENTPEHWTIKASKRLELCKDNKAYKKKFKDELYKTEKQQKKYATGSAVYAR FNKKIAQIKNRQEAYGDRLCGKQDGNPRVVATGEWNVRASVMWPASIFLYTAGWIGWAGRSYLIRTNDETKELNIDVPLA LTCMASGFSWPVAAWQEIVNGEMAVPSSQIHPGGPYTQS PsaI Symbiodinium sp. 0.019725674 1 LEVO MARPGRMLLVALAAVLGLSYCFLSSPEKLPKAKGVDFNAAVAASAALPALTMLAEDAEAKYGDNRKWSAVLVPLTTLVFP AVAMGSFVLYSFQEDAFWRLVPGTKRAAEAEKAWREHPLFKDSKDPMFGLLNPDDYEKGLEEAWERAKPAGSTVTVKDKL KQLSKQDSPHWESWRSLSA PsaJ Symbiodinium sp. 0.015832113999999998 1 LEVO MARFTNLILVAACVLLGNRFYTLLFANAPSQNLRSHVAVRAVDERDEGLVLITPEESGKVVKRDVNNNPPRIVMKTNDWD QPEIQLSTGASNQINYITPVVASDDIKAWLSLNVNFFSILALLTVGGIIEIQRFFPDTLYW PsaL Symbiodinium sp. 0.038708449 1 LEVO MRDFASVSTALTLAAVCACTVLLTGDVLAFTAGVSRGPQLPPHATGASSLAGSSMPFASAQEVMGAKGVVCFGMGFGVLL ALSRGLSQSRVSCKAEGSDIAVKEKADISKIAYLQDVPRTILEADVLEKLLMNTPRDQWEDPPEDTYLYTLKTFAEVYGP GKATKMGWWDYFRLKLDLPPGFELLDEDEMKVAADYDKLMMEGKIPFAVPGPAGFWYTGAVIQWKGKEQFAGDQVQTLTE NGRFSKQFLANLAFYRDGLKPWQRGLEIGMAHGYFLIGPFTSLGPLRNTPEAATVGLLCGCAIVGLVSIGGLIFGSTIKP TRFDKEGDKPASGFIEMINWHAIGGLGGAGFAHALITVFGS PsaM Symbiodinium sp. 0.01496978 1 LEVO MARSPLILCLVAAAVMLVAPRAFVSSPKSQNAAALTAGVAAGSMVMPAWAYDQQMMDAQLLLARVPGGKRTKELGLVVPI PEEDGLTDGQIAALFVVALVVLIAAVDLARSLYFGLQPNKFKTAKGKGSITPFMKRLIENGF PsaR Symbiodinium sp. 0.017253617 1 LEVO MGLAAAWRARSSTAAGAEGGAYKETPADERLFEQVYLQYTSEYMKGPMYWHKDKLQGSLPDYPGRPMIRDGKYTPYVLGN LKSFSSNELAFLSMLFFGVGLYGNLQFNYYDPQWAKVDAGGYFNVSYIVESLLLPISFFMHIACYIQKQNGK PsaT Symbiodinium sp. 0.01340001 1 LEVO MSRRAGSVVVLGALACLVWGPSFTGSVPRRQESALARMASSKWVNPEDPEMSHPSGLYVLPLKPAKPQENYIYTWKKGED GSIEDYVKTPFKGPERAADYYTQRKGNGAWDHWGPQGEGEA PsaU Symbiodinium sp. 0.024303311 1 LEVO MARSLAVAALIAVAGGLAFVPGAIPRGTTAPPSRALQAAPAAESSWGSLPTLVGGMALGVFFSLATLAPVRAEEAPATPA PTPAEQAPTPAPGPSDEEILAKGCDIRVDCTTKEQQFAWAKAYYRKYNQETDGKDPKYSKPSTGAGVFRKFKIDWPNPDP SIPDTTDGTYPIRNEDFLPIWKQQQEDLRAKMKEYIGREFTEIRWIGDYDNARSPYKPHNGYY CHLOROPHYLL A 0.000893489 196 CLA Chlorophyll c2 0.000608926 20 KC2 [(1~{S},5~{R})-3,3,5-trimethyl-5-oxidanyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenylidene]cyclohexyl] ethanoate 0.000642907 16 UIX (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol 0.000582855 41 DD6 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL 0.0007951159999999999 3 SQD PERIDININ 0.0006308099999999999 10 PID 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 7 LMG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 7 LHG DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 4 DGD DODECYL-ALPHA-D-MALTOSIDE 0.000510615 1 LMU PHYLLOQUINONE 0.000450696 2 PQN BETA-CAROTENE 0.000536873 13 BCR IRON/SULFUR CLUSTER 0.00035163999999999996 3 SF4 singleParticle particle 6.5 ETHANE FEI TITAN KRIOS SPOT SCAN BRIGHT FIELD FIELD EMISSION GUN 300 1.0 1.8 GATAN K3 BIOQUANTUM (6k x 4k) 50.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 2.8 FSC 0.143 CUT-OFF 161863 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_36366.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 339.19998 339.19998 339.19998 90.0 90.0 90.0 X Y Z -0.098823845 2.9602902 0.041333348 0.08881352 1.06 1.06 1.06 0.35 AUTHOR Cryo-EM structure of Symbiodinium photosystem I emd_36366_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 339.19998 339.19998 339.19998 90.0 90.0 90.0 X Y Z -0.5335106 1.8657453 0.0053185876 0.08184178 1.06 1.06 1.06 AUTHOR Cryo-EM structure of Symbiodinium photosystem I emd_36366_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 339.19998 339.19998 339.19998 90.0 90.0 90.0 X Y Z -0.52902776 1.7686827 0.005357673 0.08182303 1.06 1.06 1.06 AUTHOR Cryo-EM structure of Symbiodinium photosystem I