Cryo-EM structure of cryptophyte photosystem I

2026-09-23 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond em_admin pdbx_entry_details pdbx_modification_feature _em_admin.last_update _pdbx_entry_details.has_protein_modification 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 STRUCTURE_SUMMARY em_admin pdbx_modification_feature _em_admin.last_update _pdbx_modification_feature.ref_pcm_id DATA_COLLECTION em_admin _em_admin.last_update PDBj PDBj 2022-06-23 2023-04-12 2023-04-12 2026-09-23 National Science Foundation (NSF, China) China Cryo-EM structure of cryptophyte photosystem I Zhao LS Zhang YZ Liu LN Li K Cryptophyte, Photosystem I, evolution, PHOTOSYNTHESIS Zhao LS Wang P Li K Zhang QB He FY Li CY Su HN Chen XL Liu LN Zhang YZ Structural basis and evolution of the photosystem I-light-harvesting supercomplex of cryptophyte algae. Plant Cell US 35 2449 2463 2023 36943796 doi:10.1093/plcell/koad087 1532-298X 2109 PLCEEW 7y8a FULLOVERLAP EMDB EMD-33683 associated EM volume

photosystem I of cryptophyte photosystem I of cryptophyte 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 Chroomonas placoidea ACPI-1 Chroomonas placoidea 0.023479366999999998 1 LEVO MLRLSLLAAIVACASAFAPTSLPMGSMRKAATKGPSMQLFGAGKLQGEGVTAIPFAGRPKTPAFDGTWAGDTGFDPLTIS AWLDIRFLREAELKHCRVAMLAAAGAIAQDAFTFPGTVETFGTGKMTALHDAAVKTGTMGQMLVWIGFAEIFSTAAILQW YTDGSTRKPGDFGFDPLGFSKGKDAARLELCELKNGRLAMIAIGGMIHHYLITGKGPLELLP ACPI-2 Chroomonas placoidea 0.023400123 1 LEVO MLRVALIAAILASASAFAPMGSLGLVKSARSGAAISPRMQSGDFSAAVPFLKRPSNLDGTLAGDVGFDPLGFSDVFDLRV LREAELKHGRFAMLAVLGFLVQEVYTFPFFPKMAPVDAHDYFVTQGGGSQIIFWISFVEIFGVVALFELIQGKRDAGDFA FDPLGLGKDEATLARYKVAEIKHARLAMIAIGGFIHQFWVTKQTVLEQLGNFQSLA ACPI-3 Chroomonas placoidea 0.024966261999999996 1 LEVO MLRTLALLAAVASASAFTAAPMLSTSTRAKAVSSVSGMRMQEKSASVPFLSKPEKLDGSMAGDVGFDPLGISYFIDVKWL REAELKHGRICMLATAGILVQEVIHLPGPAFSSKFALDAWSTAPRGGMVQILIAIGLIEMVSNRFAITATDMFANPNRKP GDLGFDPLSLGANPATRAKYELSEVIHGRAAMMGLSGMIHQMIVSKQPVIDQLLNFKPVDASFKLGGAAGTMGMGI ACPI-4 Chroomonas placoidea 0.023548246 1 LEVO MLRSLALLCLVGAASAFAPGAAPLVRSNTRAAIARGPRMQEMSKAIPFAERPAKLDGKIPGDVGFDPLGFSDYYDLKYLR EAEIKHGRICMLGALGWLFPEFAKLPQFASLSTNPLKAATELGPAGWAQIFIFVGALESFSYEKIYYGDSAPGDLGFDPL RLGKNPVSRAHYEVAEIKNGRLAMIGLGGMIHHSLLTKQGAIEQIMSQNFYPSGFPQ ACPI-5 Chroomonas placoidea 0.024055030999999998 1 LEVO MLRLSLLAACIAAASAFAPVALPGMGMRAATRRPAVSMQLWEDGKVQGKGLKAIPFSDPPESLPSDMVGYVGFDPLGFST LFDIKFLREAELKHGRAAMLAAAGAIAQDIFTFPGVTSVIGDAKMTGAHDAFLKAAADGNPKANAMSQLFVWIGFFELVS MPALFETLNGGERAPGDFYFDPLGLGKGSGRARMELAEIKNGRLAMIGIGGMVHHYLLTGKGPIGTIVG ACPI-6 Chroomonas placoidea 0.022688563999999998 1 LEVO MLRVALISALVASASAFAPTALPAARASARAVSAGPKMQMSPSVPFLKRPVALDGSMVGDVGFDPLGLSSVGDIKFLREA ELKHCRLAMLAAAGSMAQDLYTFPGVDKVIGDAKMTAVHDKLVSQGAMGQLLVWIGFAEVFATMALFETLDGKRAPGDFK FDPLGFGKNPEALKRYQLAEIKNGRLAMLGFGGMVHGYFVTGKGPLELLTNFQAA ACPI-7 Chroomonas placoidea 0.024550401999999995 1 LEVO MLRVALLSALVASAAAFTAPAALFKAPTRSSRAMSVKMQDNSAAVPFLSRPAALDGSMVGDVGFDPLGFTGKYDLKWLRE AELKHGRVAMLASLGCLVQEFIHLPFEATSNPVASEAFFQVPSGGLWQIFTVIGVIEHVSNGFNMSGSTMFKSGRAPGNL GFDPLNFGKNPTARARYELAELKNGRLAMLGFAGMIHGCFITGKGPLAALTSLDWHQQIGRASCRERVGC ACPI-8 Chroomonas placoidea 0.023700525 1 LEVO MFARTLLLAACAASASAFAPGSFAPMGLRGSTAAVSRPMARAGLSSVSMAANPMTNAIEEFAESAPELASRGLGVTTNAE RWNGRHAMFGIFAIVMTAYFKGHGLIPDAEKILDVNQWGPLASAGQGQGITNERAIILIAHVHVLVVSVLAAFAPFQFQD TLVKEKGYTPEAPAGIIPPFKTGLTPEAELINGRLAMLGVISIIMASIFTGNSVIDVVNLGLGKILF ACPI-12 Chroomonas placoidea 0.023223098 1 LEVO MFRALLVLAAVAGASAFTAPAVLPGRSTARAATKGPSMQLYKEGSLQGKGVNCIPIFKRPDSLKGDAVGDMGFDPFGFSS WVDMNYVREAEIKHGRIAMLAFAGIVVEVLGIKAPGAGKILGSSTDIFEIHNAAVEKGSMGQILLWCGFFEMTAGLPAMQ QMLEGSGRTPGDFGFDPLGLGKKDFAQMQIKEIQNGRLAMLAVSGMVHHALINGKVQGLP Photosystem I P700 chlorophyll a apoprotein A1 Chroomonas placoidea 0.08349357 1 LEVO MTVSSTEQEAKKVSITVDKDPVATSFEKWAQPGHFSRTLAKGPKTTTWIWNLHADAHDFDSHTSSLEDISRKIFSAHFGQ LSIIFLWLSGMYFHGARFSNYSAWLSNPTAVKPSAQVVWPIVGQEVLNGDVGGGFQGVQITSGFFQIWRASGITSEVELY WCALAGLLMSGLMIFAGWFHYHKAAPKLEWFQNAESMLNHHLSGLLGLGCLSWAGHQIHVSLPINKLLDAGVAPQEIPLP HEFLVNRDLMAQLYPSFSKGLVPFFTLNWSEYSDFLTFKGGLNPVTGGLWLSDTAHHHLALAVLFIVAGHMYRTNWGIGH SMKEILEAHKGPFTGEGHKGLYEVLITSWHAQLSINLAMLGSLSIIIAHHMYAMPPYPYIATDYPTQLSLFTHHMWIGGF CVCGAAAHAGIFMVRDYNPAQNYNNLLDRVIRHRDAIISHLNWICIFLGFHSFGLYIHNDTMRALGRTQDMFSDTAIQLK PVFAQWVQNIHTVAPGNTTPNALATASYAFGGNVVSVGNKVAMMPISLGTADFMVHHIHAFTIHVTVLILLKGVLFSRNS RLIPDKANLGFRFPCDGPGRGGTCQSSAWDSVFLGLFWMYNCISVVIFHFSWKMQSDVWGTVQADNTVTHITGGNFAQSA ITINGWLRDFLWAQASQVIQSYGSSLSAYGLIFLGAHFIWAFSLMFLFSGRGYWQELIESVVWAHNKLNFAPAIQPRALS ITQGRAVGLAHYLLGGIGTTWAFFLARIISVG A0A222AIB4 1.97.1.12 Photosystem I P700 chlorophyll a apoprotein A2 Chroomonas placoidea 0.08221982 1 LEVO MATKFPKFSQALAQDPATRRIWYGLATAHDFESHDGMTEENLYQKIFASHFGHLAIIFLWTSGNLFHVAWQGNFEQWVLN PLKVKPVAHAIWDPHFGQPAVKAFTKGGVFYPVNIATSGVYHWWYTIGMRTNNDLYAGSLFLLFLSGVFLFAGWLHLQPK FRPGLSWFKNNESRLNHHLSGLFGFSSLAWAGHLIHIAIPEARGQHVGWDNFTKTLPHPAGLTPFFTGNWSLYADNPDTA NHIFGTSEGSGSAILTFLGGFHPQTQALWLTDIAHHHLAIGVVFIFAGHMYRTNWGIGHSLKEILDAHRPPGGRLGAGHK GLFETITNSLHFQLGLALASIGVITSLVAQHMYALPAYAFIAKDYTTQAALYTHHQYIAGFLMVGAFAHGAIFFVRDYDP EQNKNNVLARMLEHKEAIISHLSWVSLFLGFHTLGLYIHNDVVVAFGTPEKQILVEPVFAQWIQASSGKALYGFDVLLSS SNSVATNASNNIWLPGWLDAINSGKNSLFLPIGPGDFLVHHAIALGLHTTALILVKGALDARGSKLMPDKKDFGYSFPCD GPGRGGTCDISAWDAFYLSMFWMLNTIGWVTFYWHWKHVTIWQGNAGQFNESSTYIMGWLRDYLWLNSSPLINGYNPFGM NSLAVWAWMFLFGHLIWATGFMFLISWRGYWQELIETLAWAHERTPLANLVRWKDKPVALSIVQARLVGLIHFTVGYVFT YAAFVIASTTGKFG A0A222AI95 1.97.1.12 Photosystem I iron-sulfur center Chroomonas placoidea 0.008743131 1 LEVO MSHAVKVYDTCIGCTQCVRACPCDVLEMVSWDGCKAGQIASAPRTEDCIGCKRCETACPTDFLSVRVYLGGETTRSMGLA Y A0A222AI25 1.97.1.12 Photosystem I reaction center subunit II Chroomonas placoidea 0.015590765 1 LEVO MSETLNLQIPSPTFEGSTGGWLRAAEVEEKYAITWTSGKEQVFEMPTGGAAIMRKGENLLYLARKEQCLALGTQLKTGFK ITDYKIYRIFPSGEVQYLHPKDGVFPEKVNAGRIGVGNVSHSIGKNLNPSQIKFTNKSFNG A0A222AIA6 Photosystem I reaction center subunit IV Chroomonas placoidea 0.007352386999999999 1 LEVO MVKRGSQVRILRKESYWYQDVGTVATIDTSGIRYPVVVRFEKVSYSGVNTNNFSLDEVVEVVKK A0A222AIF3 Photosystem I reaction center subunit III Chroomonas placoidea 0.020393484 1 LEVO MKNWVSLVLIFSIVTTPYVAHADVAGLTPCKDSKDFQRRLDGSVKKLKTRLAKYEKGTPPALALEKQIERTQARFERYGK AGLLCGTDGLPHLITDGRWSHSGEFVIPGLFFLYIAGWIGWVGRSYVLFARESDKPTEKEIILDVPAALSFVSTGFIWPV SAFKEFTSGNLIADESEITVSPR A0A222AI52 Photosystem I reaction center subunit VIII Chroomonas placoidea 0.003975751 1 LEVO MTAAYLPSILVPLIGLIFPGFVMGFAFIYIEQEEIA A0A222AI78 Photosystem I reaction center subunit IX Chroomonas placoidea 0.004862727 1 LEVO MDSNFLKYLSTAPVLLTVWLSFTAGLVIEANRFFPDMLYFPM A0A222AI55 Photosystem I reaction center subunit PsaK Chroomonas placoidea 0.008836370999999999 1 LEVO MNADLLLAVVPQTAAWSAKTCSVMVISNLLCIVAGRYVIQVKGSGPSLPLTGSFSNFGLPELLATTSLGHIVGSGAILGL SYVGLLS A0A222AI34 Photosystem I reaction center subunit XI Chroomonas placoidea 0.016490883 1 LEVO MAQFVKPYNDDPFVGNLATPVSTSSFTRSFLSNLPAYRSGLSPLLRGLEIGMTHGYFLVGPFYKLGPLRNSDVALISGLF SSIGLIIILAACLAIYGVVSFNEDDNTDSLQTSRGWKQFTSGWLVGSIGGASFAYILISNIVFLQTSGLNLIK A0A222AI68 Photosystem I reaction center subunit XII Chroomonas placoidea 0.003247952 1 LEVO MISDTQIFVALILALVSLVLAIRLGTALYQ A0A222AI28 PsaO Chroomonas placoidea 0.01625303 1 LEVO MKVAFLVLLAAATANAFAPTAAFLPKAHGIAASKPAMALRAAPRAVAKPLAVQAKFEISDGVEFDLNPLVLAISFLGWSL PGLLPSNIPLYGGKGLTTALFAEIGEHLQTFPAPPPIGDPFWVILFIWHSGLFATMIFGTIGYNGYGPKSTTKY PsaR Chroomonas placoidea 0.013867048 1 LEVO MVRALCFLALIASAAAFSTAPGLALRSSVRPATSTKTPMKMAGYSPVPSPDNTKETYWETKAPSSQVLGIGKDVSSGNYI VASVVAAVVGAACTGQCIPLTVSPNPVFILGSFLLPYSWALHVAAWIQRNNGK Unk1 Chroomonas placoidea 0.013975214

Authors do not know how the coordinates align with the sequence and the residue numbering is arbitrary.

1 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) (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) (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) ACPI-S Chroomonas placoidea 0.025645455 1 LEVO MAQAAPPSKLPENMAKKNALKVNKEQWGIEEAIKVDAKAAAPAPKAAAPAPKKAAPKKGAAPAEATVGFSGVPSDFCRPA PTAFPAEPAGMTVFGARGPRAEGHRDKFGSRHAAVSLACAALLWQPISQAGMYSIDSGSLAKKSFSEMEVPGFGDAKKVP TIESFFPFTKNGFDASPALFGKDSMIVFENPLGKCGAYASSCHTFLDEMGDMLKATPQEMPRSKAAPTYSFPWMYDHAAW KK ACPI-13 Chroomonas placoidea 0.022270991999999996 1 LEVO MIRAVILAGCVAAASAFAPGASLVGARAATRAVSAAGPKMQMSPSIPFLKKPDALDGTAAGDIGFDPLGFSSLADIKFLQ EAEIKHCRIAMLAAAGSIAQDIFTFPGYSALTGGAKMTAAHDKLVATGTMGQILFWVSFAEVFGTVALFDTLDGKRAPGD FKFDPLGMGKKNMADMQLKEIKNGRLAMLGIAGMTHGYFISGKGPLELLGNFPTA ACPI-14 Chroomonas placoidea 0.023755605 1 LEVO MFRAALLLACLASASAFAPGSLMMPKSATRAAISRGPRMQANDDLAVPFLERPPMLDGSYAGDIGFDPVGFSNYFDLRWL REAELKHGRVCMLGVVGFLVQEFVTLPMFSNGVTPVDDFFVVPATGLWQIFFTIGFVEAFSNGFKLTPSDMFADDRAPGD LGFDPLGCGKDPAALARRQLVEVKNGRLAMIAFGGMLHQQLLTKQGVIEQLTNFKAIM CHLOROPHYLL A 0.000893489 222 CLA Chlorophyll c2 0.000608926 14 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 47 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 2 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 7 LMG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 19 LHG 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL 0.0007951159999999999 2 SQD (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene 0.000536873 24 8CT DODECYL-ALPHA-D-MALTOSIDE 0.000510615 3 LMU IRON/SULFUR CLUSTER 0.00035163999999999996 3 SF4 PHYLLOQUINONE 0.000450696 2 PQN DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 2 DGD 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 2.71 FSC 0.143 CUT-OFF 118810 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_33683.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 -0.0650245 1.9881129 0.03284991 0.057182882 1.06 1.06 1.06 0.3 AUTHOR ::::EMDATABANK.org::::EMD-33683:::: Cryo-EM structure of cryptophyte photosystem I emd_33683_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 -0.31896555 1.307922 0.0020833565 0.043045335 1.06 1.06 1.06 AUTHOR ::::EMDATABANK.org::::EMD-33683:::: Cryo-EM structure of cryptophyte photosystem I emd_33683_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 -0.30174935 1.2555094 0.0020003768 0.042942163 1.06 1.06 1.06 AUTHOR ::::EMDATABANK.org::::EMD-33683:::: Cryo-EM structure of cryptophyte photosystem I