Cryo-EM structure of haptophyte photosystem I

2026-08-12 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY 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 EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update PDBj PDBj 2024-04-10 2025-01-22 2025-01-22 2026-08-12 National Natural Science Foundation of China (NSFC) 2023YFA0914600 China Cryo-EM structure of haptophyte photosystem I He FY Zhao LS Li K Zhang YZ Liu LN Haptophyte, Photosystem I, evolution, PHOTOSYNTHESIS He FY Zhao LS Qu XX Li K Guo JP Zhao F Wang N Qin BY Chen XL Gao J Liu LN Zhang YZ Structural insights into the assembly and energy transfer of haptophyte photosystem I-light-harvesting supercomplex. Proc.Natl.Acad.Sci.USA US 121 e2413678121 e2413678121 2024 39642204 doi:10.1073/pnas.2413678121 1091-6490 0040 PNASA6 8z11 FULLOVERLAP EMDB EMD-39717 associated EM volume

Photosystem I of haptophyte Photosystem I of haptophyte 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 31 Isochrysis galbana iFCPI-7 Isochrysis galbana 0.022841299 1 LEVO MLSIALSSLSYSPAAMPAVQVSRGAVNMAIAKPSNAVPFLTAPPCQSSKLAGAETGFDPLYLSEFIDLKWAREAELKHGR ICMLAAPGYFFQEFFQLPGFPGYSPNGIEAVSSVSPEALAQIVIFMSVIEYNSNLNKWTMDTMFADPKREPGNLGFDPLK FGENKNTRARLEMAELKNGRLAMLAFSGMVHQTFVTGKPVWASLQDIFA iFCPI-1 Isochrysis galbana 0.022262721 1 LEVO MLSISVGSLSLATPMRPVVAPRAPVPKASIFEAGMAQYNADYPWLAKYGFGPSVKAERWNGRHAMFGWVAILATGVAKSH GLLPAGDLMLTYQDWGGLAQQGFNTYISNERAVIMIAHVHALAVSFAAAFGPQVLGDSLTLLDGEKDEEPYGFLPPMQFG LTPAAEIANGRMAMFGLISLVCTSAFTGMDILQIVDIGTGGNLLTHPMF iFCPI-11 Isochrysis galbana 0.02188949 1 LEVO MLSLVSASPSLLAPVVTPRAPAPAMAAERSASIPFLKKPPALDGSMIGDVGFDPLGFSTTITELGGDLSYVREAELMHGR QAMLAAVGMIFPKVFGKLPAPWTEAVSTNPLEAQYQLPPVVLGQILISIFIAEGLRSRIVFGNDPNYVVGDHGFGSNFLK GKSEAQIADMKLKELNNGRLAMIAVTGMFFQISIKGNLWPIIDGF iFCPI-6 Isochrysis galbana 0.026300061 1 LEVO MALRTLAVSVGVATALSTGATPAALARPKMTAHADALRFLRMDEAAPAKPAEEAEEAAAPAPPPAPPPVEYSESLPFLVK RKALKGYVGDVGFDPLGFSEILPMDWLREAELKHCRVAMLATFGFGFTDFWHFPGFDYTTLEAHDACVASGAMSQLLLWI GLLEVFGTIGIDQTLRGSGRAAGDFGFDPLGFGSDPAKMADLQMKELANGRLAMFAFSGFVTQSVLTGNQFPYLFDYQTT DVFAL iFCPI-5 Isochrysis galbana 0.021683213 1 LEVO MLSLASAPLSFAGPALSGVAHRTGALNMMAKSKSIPFLEAPPALDGTMAGDKGFDPMRLSEVVPIQWAREAELKHARICM LAVVGWVAVDLGFTVPYAPQVSSLAAHDAAVEKGAFLFLLFPIAVVEVLAGIPKCFQIMNDPNAAPGGDYKFDPLGIGAS ADMQEKEISNGRLAMMAFSGIVTQAALTQAPFPYTYNGMSDLVPVL iFCPI-8 Isochrysis galbana 0.025390158 1 LEVO MLSVVSAPTLAFGAGVARVVPQRAAVQMSAGPMYDEPLAPSGMGREFINKERAPLSSYVGASQELAAFPGGGGKEGMAPT PWDPFCFSELYKVSANNPDVAWLRESELKHGRMAMLAITGVMVQSTGFHLPGNAEVSFANSDWVSAPTTLPPVVWGQVLA FVAIAEGQTSEGLFDLWLGDTSKREPGNLGWGSGLLSKDKKAADKMRLKELKNGRLAMLAIMGVAANHFIPGALPGCIYS iFCPI-13 Isochrysis galbana 0.020749141 1 LEVO MLSLASLPSTAFVAPIPAARLGVRAAAPLMGVEDMVGASVEVSNKVWDPLKLSAKMDEGNLNLVRAAELKHCRVAMLATV GWAWTATGTHFEGMLSTSQGISFADACAAGPLLGAAKVPAVGVWQIIAAIGALEVFWENKYPASECAGNFGVPWVTSDPA KMKEIQLAELKNGRLAMIGIISFACAESIPGSVPFYPF iFCPI-10 Isochrysis galbana 0.021410861 1 LEVO MLTLSLQSLSLNAGVAPAARVQRMQAPMMVKSQALPFLEAPAKLDGSMAGDKGFDPLNLAGSFDINWMREAELKHGRICM LAWVGYVAVDNGFYVPFAPHVSSLAAHDTAVKSGQMLFLLGAVGVVEALSYNAINEMMSGQTDRRPGDFSMDPFKMVDTP EKAKSMLEKEISHCRLAMMAFSGVVTQSALTGHGFPYL iFCPI-3 Isochrysis galbana 0.02105566 1 LEVO MALSLLASPLALVNNGMLRAPVMQPACQGIQAKLDMVGACKPLGFFDPLGFSKDASPASMAKFREAELKHGRVAMLACAG MITADKFHPLYDGKLSSNPLLAIAQVPKLGLLQILLFIGFMEVFGILNSRRPDYKPGDFLGSSQWDTTEVWDNYQLRELN NGRLAMFASIGMLTHAYITGKGPLELLDGSSIVF iFCPI-9 Isochrysis galbana 0.020788168 1 LEVO MLSLTSAPLAFSAPLAAPLAPQRAAVSMMAKSQALPFLEKPASLDGSMPGDVGFDPLGLSSYFPLDWMREAEIKHGRVCM LAIVGYIAVDIGIRAPGAEKLGSLTSFTAHNAAVTSGHMWALLGVAGIAEIAGMAGIAATLNGSGRAPGDFAFDGGFAKD AAKLERFKLSEIKHCRLAMMAFSGLVTQDAMANGMGFPYF iFCPI-4 Isochrysis galbana 0.021735281 1 LEVO MLSLTSASALALHAPLAAVPTAQRAAAAPLMAMENELGATGPLGYWDPLGFSTKQPERFARYRAVELKHGRIAMAACTGY FVQSVLRWPGYLSTSAGVKFSDLPNGIAGFAKIPPLGLAQIFLFIGLMEAFTWPFYQGGLGKVPEGKLPGDVAGDLWVRY SDPEVKKHKLNVEINNGRAAMMGSLGMLMHDHILGTWIPPGF iFCPI-12 Isochrysis galbana 0.024225039 1 LEVO MLSLALAPLSFNAPMAPLSQAMRSSTSVRMGVETMEGAAGPETAGKVFDPLGLASLGGEETLAFFRHAELKHGRVAMAAI VGFQFHINHVHFPGYLSPSAGVTFEQLAGVGPFEAWNLIPLLGKMQILFTIAGLEHASECLDPAGHYTKGGTPGNLKFLK KFWDTPGFTDKLTEEQKATKRVSELKNGRLAMIGMASIISAMSIPGSVPLLNGAPALTGTGFVLPFGDF iFCPI-15/14/16 Isochrysis galbana 0.023142911999999998 3 LEVO MAPALINAPVMPVAGAARVAVPKMAFVDSIEGVGEETGNKIWDPLGISDAVSDEAVMWFRHSELKHGRVAMLATVGYMIG AAGITFPGEIAKGVTFASVGASGPYAAWDATPTAGKLQILTIILALEWAAETKKPHYMRGGVPGKIDQLPFEGIPGLWAP KIKFWDPLNFMGALTEEQKARKRKSELKNGRLAMIGIISFLTGHNIPGSVPALDSHF iFCPI-17 Isochrysis galbana 0.023706856999999998 1 LEVO MALSLASPLACGLAAPAMVRPAVQTRHVMMSAADGMEGISHETGMKTWDPLGLADLGSPATLAFFRHAELKHCRVAMAAF VGWLVAVSGVHFPGLCSFSEGVSFEDISKLTPLEQWAAVPALGKAQILLAIGIIEHNSEWKIKPHYMAAGGKPGDLKGLK SFWDPAGLTSKMSAAKLERQRLSELKNGRAAMIGIISVLIAHNVPGSIPLPINFPAGPSLILPF iFCPI-20/19/21 Isochrysis galbana 0.021494846 3 LEVO MLSIAVSSLSFNAPALAPRTAPSAASVRMGVADMEGVGPETGNKVFDPLGLAKIASPETLAWYRAAELKHSRVAMAAVTG WAWVSSGGPLFPGYLSIDQGITFESLGRDGYAAWAAVPEAGKFQILGTIGILELLQEGSVKPHYMAGGTPGKVPLLWDPL GFTTKLSADTLATKRTSELKNGRLAMIGVMSLVSAHFIPGSVPLLP iFCPI-18 Isochrysis galbana 0.020023943 1 LEVO MLALSSMPLAFSAPASAAVAAAPRAAVSMGGNVNNMIGKYSVKGTVYDPLNLASTYDNNWLREAELKHGRLCMLAFAGFI ANDAGWGLPGLDIKCSSVEAHDKMVESGHMWALLAFVSVCEALHFSVIIPKLDGDWGDYEPGNYGLDPFKLDTPARREAE LKNGRACMLAFSGIVTQAALGHPAPYW iFCPI-22 Isochrysis galbana 0.025384162 1 LEVO MLSLASAAPLAFSAPIAAAVQPARAGAASMLTKEKLAEKLNPAIGYYDPLGLATADFWSQGNDATWGFLRHSEIKHGRVA MAAFVGFCVQSNGIHFPFDFQGGGVSQAQYAAGLSPPEQWDALPFAAKAQIILFIGFLEWWSEFGGQHYMRGGQPGKYPE FKNIPLHKMPNLFDPLGLSKGLSAEQRETKLCAEINNGRLAMLGVFGFYCAEKIPGSVPLLSFIKPYAGEIMGPF iFCPI-2 Isochrysis galbana 0.021908445 1 LEVO MLSFALSPLALNVAPMGAVASPRATVAMMAKSKSMPMMDAKEHLQGMVGNVDFDPLGLSTPENIKWMREAELKHGRMAQL AWAGYVAVDLGLRFPGEKYAGLTSLSAHDATVGYELFLLLLLVGTFETIGGKQIYDMQMSGANREAGDFGFDPLMLLKSP NAEKYKLAELTHGRAAMIAFSGVVTHSALPDAFGYGKATFPYF L-iFP Isochrysis galbana 0.01256768 1 LEVO MAKLLFLLIGVLASVVSGLVVGTAARSAVRAEQPAMSESRRSVLAAALFLAPAAASAMTIPGVNAPGLVPATKKSVGPKP EWDSFRDTSHFWSSEGIMNSVPKVKGIVTPKTPVGYGAPPKN Photosystem I P700 chlorophyll a apoprotein A1 Isochrysis galbana 0.083558156 1 LEVO MKVGSKELEASKVRVIVDKDPVATSFEKWAQPGHFSRTLAKGPKTTTWIWNLHADAHDFDSQTSSLEDISRKIFSAHFGQ LAIIFLWVSQAYFHGARFSNYSAWLQNPTAIKPSAQVVWPIVGQEILNGDVGGGFSGVQITSGVFQMWRASGITNETELY WTAMGGLVMSALMVFAGWFHYHKAAPKLEWFQNVESMMNHHLAGLLGLGCLSWSGHQIHISLPINKLLDAGVAPQEIPLP HELLFNQDLMAQLYPSFKKGLLPFFTLNWSEYSDFLTFKGGLNPITGSLWLSDTAHHHLALAVLFIFAGHMYRTNWGIGH SMKEILEAHKGPLTGEGHKGLYEILTTSWHAQLAINLAMMGSLSIIVAHHMYAMPPYPYIGVDYPTQLSLFTHHMWIGGF CICGAAAHGAIFMVRDYSPVQSYNNLLDRVLRHRDAIISHLNWVCIFLGTHSFGFYIHNDTMRALGRPQDMFSDKAIQLQ PIFAKWVQSLHTLAPGSTAPNALATSSYAFGGDVVAVNGKIAMMPITLGTADFMVHHIHAFTIHVTVLILLKGVLFARSS RLIPDKANLGFRFPCDGPGRGGTCQVSAWDHIFLGLFWMYNCISVVIFHFSWKMQSDVWGTISSSGKISHVTGGNFANSA LTINGWLRDFLWSQASQVIQSYGSALSAYGLIFLGAHFIWAFSLMFLFSGRGYWQELIESIVWAHNKLKLAPAIQPRALS ITQGRAVGLAHYLLGGIGTTWSFFLARIISVG A0A7D4XMT1 1.97.1.12 Photosystem I P700 chlorophyll a apoprotein A2 Isochrysis galbana 0.082181125 1 LEVO MATKFPKFSQALAQDPATRRIWYGIATAHDLESHDGMTEENLYQKIFASHFGHLAIIFLWTSGNLFHVAWQGNFQQWVLN PLKVKPIAHAIWDPHFGQSAIKAFTRGGVSYPVNIATSGVYHWWYTIGMRTNEDLYFGALGLLILSTALLFAGWLHLQPK FRPGIAWFKNNESRLNHHLSGLFGVSSLAWAGHLIHVAIPESRGQHIRWNNFTSTLPHPEGLTPFFTGNWGLYAENPDTA QHIFGTSEGAGTAILTFLGGFHPQTQSMWLTDIAHHHLAIAVVFIFAGHMYRTNWGIGHSMKEILDAHVPPKGRLGSGHR GLFETITDSLHMQLGLALASLGVATSLVAQHMYALPSYAFMAKDYVTQAALYTHHQYIAGFLMVGAFAHGAIFFVRDYDP EVNKDNVLARMLQHKEAIISHLSWVSLFLGFHTLGLYIHNDVCVAFGTPEKQILFEPVFAQFIQAASGKALYGFDVLLSS PTSVATVAGSKIWLPGWVEAINSGKNSLFLTIGPGDFLIHHAIALALHTTTLILVKGALDARGSKLMPDKKDFGYSFPCD GPGRGGTCDISAWDAFYLAMFWMLNTIGWVTFYWHWKHMTIWGGNAAAFNESSTYIMGWLRDYLWLNSSPLINGYNAFGM NAQAVWAWMFLFGHLIWATGFMFLISWRGYWQELIETLVWAHERTPIANLVKWRDKPVALSIVQARLVGLAHFTIGYIFT YAPFVIASTTGKFS A0A7D4X9X4 1.97.1.12 Photosystem I iron-sulfur center Isochrysis galbana 0.008795143 1 LEVO MSHSVRVYDTCIGCTQCVRACPCDVLEMVPWDGCKAGQIASAPRAEDCIGCKRCETACPTDFLSVRVYLGSETTRSLGLS Y A0A7D4X9R7 1.97.1.12 Photosystem I reaction center subunit II Isochrysis galbana 0.015882163 1 LEVO MTTDLLNLQIPSPTFGGSTGGWLRAAEIEEKYAITWTSKKEQIFEMPTSGAAIMQKGENLLYLAKKEQCLALGTQLRTLF KISDYKIYRIFPNSEVQYLHPKDGVFPEKLNEGRVGVGNIGYSIGKNPNPVNVKFTGKNTFD A0A7D4XG42 PsaE Isochrysis galbana 0.012835604999999998 1 LEVO MLRSIALFALAGSASALAPSAIGSSRVATRAGSPEMISRGSVVRIMRPESYWFQECGSVATIAKGGDRYPVVVRFEKVNY AGVATNNFAMDELVEVEAPPAKAAPAKAEAPAKEAAEAAPPAEA Photosystem I reaction center subunit III Isochrysis galbana 0.020218377 1 LEVO MKTFFNWFLAISIFTTAPTLVSADVSGLTPCKDSAVFKRRLDGSVKKLNSRLANYTEGTPAYIALEQQIEQTKARFAKYG EKGLLCGADGLPHLIADGRLDHAGEFIIPGFGFLYIAGWIGWAGRSYLQFSKKTDKPNENEIIINVPVALGMMAGAFIWP LAAWKELIDGKLLVPGDEITVSPR A0A7D4XMU0 Photosystem I reaction center subunit VIII Isochrysis galbana 0.003943706999999999 1 LEVO MSASFLPSILTPLVTLVFPGLCFALFFVLIEQDEIA A0A7D4X9U5 Photosystem I reaction center subunit IX Isochrysis galbana 0.004506287999999999 1 LEVO MSNDLLKYLSTAPVLLTAWMSITAGIIIEIQRFFPDSLSF A0A7D4X9Y3 PsaK Isochrysis galbana 0.009484241 1 LEVO MLDAGHAVDTASQLMAMSLPIPAYSIPKAFIMMFCNVLVISTMTIQGKGLAKGTPHDEMVESFGITWLLAGTALGHIVGA GTILGCSTAGIL Photosystem I reaction center subunit XI Isochrysis galbana 0.015477796 1 LEVO MSEFVKPFNNDPFVGNLSTPVTTSTATKLYLGNLPIYRKGLSPLMRGLEVGMAHGYFLIGPFYILGPLRNSPNALLVGLF SAYGLIIILTLALTIYGLASFQDNSTGSNLESSKGWRSFTSGFTVGALGGASVAYVLLNNVSFFA A0A7D5B6G5 Photosystem I reaction center subunit XII Isochrysis galbana 0.003149833 1 LEVO MITDGQIFVALCIALTAAILAIGLGRQLYV A0A7D4XMW6 PsaR Isochrysis galbana 0.013750825999999999 1 LEVO MHTVAALLCLIGSASALAPAARVVPVVQRAVAPAVRVAPAAMLDRSEAADTWWGDKDYPSSVVLGIGKDVPSSIYGVTSA IAFSVGAYCIAQSNIINILSGSTVNGFYVAGALLVPYSWGLHVAAWIQKQNGK CHLOROPHYLL A 0.000893489 280 CLA Chlorophyll c2 0.000608926 62 KC2 (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol 0.000582855 51 DD6 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 16 LHG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 20 LMG (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate 0.0006589059999999999 54 A86 DODECYL-ALPHA-D-MALTOSIDE 0.000510615 5 LMU 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL 0.0007951159999999999 2 SQD DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 2 DGD BETA-CAROTENE 0.000536873 20 BCR IRON/SULFUR CLUSTER 0.00035163999999999996 3 SF4 PHYLLOQUINONE 0.000450696 2 PQN singleParticle particle 6.5 ETHANE FEI TECNAI F30 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 2.74 FSC 0.143 CUT-OFF 148236 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_39717.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 423.99997 423.99997 423.99997 90.0 90.0 90.0 X Y Z -0.18227711 5.577181 0.06502798 0.12944712 1.06 1.06 1.06 0.5 AUTHOR ::::EMDATABANK.org::::EMD-39717:::: Cryo-EM structure of haptophyte photosystem I emd_39717_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 423.99997 423.99997 423.99997 90.0 90.0 90.0 X Y Z -0.7492274 2.9270592 0.0036065874 0.11551633 1.06 1.06 1.06 AUTHOR ::::EMDATABANK.org::::EMD-39717:::: Cryo-EM structure of haptophyte photosystem I emd_39717_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 423.99997 423.99997 423.99997 90.0 90.0 90.0 X Y Z -0.77205515 2.8924222 0.0036252588 0.11549046 1.06 1.06 1.06 AUTHOR ::::EMDATABANK.org::::EMD-39717:::: Cryo-EM structure of haptophyte photosystem I