Cryo-EM structure of the Chromera velia PSI supercomplex at 1.84 Angstrom resolution

2026-03-18 REL PDBe 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 _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 _em_admin.last_update PDBe PDBe 2025-01-10 2026-01-28 2026-01-28 2026-03-18 European Research Council (ERC) Synergy Award 854126 European Union Cryo-EM structure of the Chromera velia PSI supercomplex at 1.84 Angstrom resolution Yuan X Qian P Sobotka R Naschberger A Photosynthesis, Photosystem I, PSI-FCP complex, Chrome velia, Cryo-EM. Yuan X Lukes M Qian P Charras Q Smrcka T Man P Kovarova L Konik P Heilmann E Al-Amoudi A Sobotka R Naschberger A The cryo-EM structure of Photosystem I from Chromera velia with a bound superoxide dismutase heterodimer. Nat Commun UK 17 913 913 2025 41423677 doi:10.1038/s41467-025-67637-0 2041-1723 EMD-52514 focused EM volume

FCPa_region focused

EMD-52517 focused EM volume

FCPe_region focused

EMD-52501 focused EM volume

SOD_region focused

EMD-52507 focused EM volume

Psa35_regoin focused

EMD-52508 consensus EM volume

Consensus map

9hyu FULLOVERLAP EMDB EMD-52514 focused EM volume

FCPa_region focused

EMDB EMD-52517 focused EM volume

FCPe_region focused

EMDB EMD-52501 focused EM volume

SOD_region focused

EMDB EMD-52507 focused EM volume

Psa35_regoin focused

EMDB EMD-52508 consensus EM volume

Consensus map

EMDB EMD-52518 associated EM volume

Cryo-EM structure of PSI super complex from C. velia

PSI super complex from Chrome velia PSI super complex from Chrome velia 0 1 2 8 3 4 5 6 7 9 10 11 12 13 15 16 17 18 19

A complex containing PSI as a core with other components for example PsaA-, PsaB, Psa

Chromera velia RM12 0.6544 Superoxide dismutase [Fe] Chromera velia RM12 0.041899281000000003 1 LEVO MRVHPVVAVSGLGVSAVSAFVFRGTPSAGIPRASPAATELSNYPERVAKEPGWAKVEYEIGGIGWSNPAIDEANENITKK MQANGETIFNLWAPWDQAQVRTQDAPSYRELMDVVDFTWQIPGTERWWYDLNIDDAVRMQPFPLERIRFDPRNLQPHRFP EQVFDHLAEYHAPYVRKLKALVEGTPLEKESLEELASRKTRNETIDNAVGMCYNTGLYWESLSSKSDWGGDQWAHGPLKE KIEKKYGSLKGFKDAVVTAGMALFGSGHLWIVSDKTGEVDIVTTSDASNPMREGKGYPLLVCDLWEHAFYEDFRNDKKKA LTSWLNLMNWQKGNKRLETYMEKMKLKDLAPTPAQEMKPKEPEPTPGPAA A0A0G4HJZ8 1.15.1.1 Superoxide dismutase [Fe] Chromera velia RM12 0.029931839999999998 1 LEVO MRFATLSLLGFFGASEAIRSRDLQAFVVSAPGASSPSRRSPATALDAVAVGSNVYEKMGVSTLVSGEEGPFKLKELPWFP TVLAPMMSYETISYHYGKHHALYVRNLNALAKEDSSLASKSLEDIFKGAEKGKKLFNQAAQVWNHDFFWNSMSPEGGDES FSETSKVKSAIISQWEDLGKFKEEWVKLALKHFGSGWIWLVQQKDGKLAIVDTHNAMNPISENLGTPLMTMDIWEHAYYV DHKSNKGLYTASFFEVCNWDFAEKNME A0A0G4FB02 1.15.1.1 photosystem I Chromera velia RM12 0.044801406 1 LEVO MPLNGLLAVQLWFFGTVSILVAHVMFAFPPYPFLAQNYATQISLFTHHMWIGGFLLVGSGAHASLYLIREQGDLTRTNSL VALCLNYRDAIISHLNWLCIFLGLHSFGIYIHNDTLAALGRFDDQITNLPPLGAEWFQHAVTANFPINNGFKNHFNTQIL MNDKIVFSNLSFNTADFLVHHIHAFTIHVTVLILVKGILFSRDSNLISDKYALGFRFPCDGPGRGGTCQVSGWDHIFLAL FWMYNSISVVIFHFFWKVQSDVWGYQSLDNGITHITNGNFTKSALTINGWLRDFLWAEAAQVVQSYSTPFFVYGLVFLGA HFIWAFSLMFLFSGRGYWQELIDYYTYAVYKWSQLPYLAFQALSIVQGRAVGLAHYLLGGIGTTWAFFLARALTL D9IXI2 1.97.1.12 Photosystem I iron-sulfur center Chromera velia RM12 0.008961316 1 LEVO MHNVGIYTTCIGCTQCVRACPTEVLDMMTWDHCRAQQIACSDTLQDCIGCKRCETACPTDFLSIRVELGTENYYSMGLAY D9IXG0 1.97.1.12 Photosystem I reaction center subunit II Chromera velia RM12 0.030636371 1 LEVO MKFLAVAALICVGGARAFVAPSAPSNRQLATELRAGVPANPKPGSQFDLSVPDKDTLIRRRGGRGWLGKANNYGRFLISW THNKAEPFPCPTGGSSLMKPGANRLLLAKKEQGIALGRWLKRTLKIDNWKIFEIKPDGTVIFRSPKDGIYPEKKDPERVK RLTLLGSSYDNQERMARYSARKQFRSYEKYLKEQGEMATWQYILQRFRAESIQAFDADFGDMDVQEAQREGYAKMRAEKQ KEMGEGVISPAMIQMYMQILKDPYKGRRD A0A0G4H942 Photosystem I reaction center subunit IV Chromera velia RM12 0.014430821 1 LEVO MKLASALLLLCLSATCAFARRLSGFLSGLPSRQRDGARQATVLEAIQKGSKVLILKPESYFYGFTGDVVVVDKNPFYPYG VTVKFPSMQYKGLNTFNFKLDELQEVAPPAPKKKKKKAAVNPAAEPAEPAASS A0A0G4H6U3 Photosystem I reaction center subunit III Chromera velia RM12 0.035865297 1 LEVO MRVSLCMAIGAASVASEASAFVAPPSRMGRGLLSSQLRAERPSKTEASEARSKEFDESIFDQAMLEDDDSAFDPMMDFAR LATPAAIAMAAATVAPQVAHAADATLVPCAESKRFQTIMKAEIKANEKRVKENPKGSFFRDQFIAELKRSKIRKWRFEHS SLMCSKEDGKPRVDVTNPNQIFGGFFAFVYVLGAIGWSAKTYNRGIKAAYGPDGGWKEVILDWPFVLQVFYHSLGWPGRT WKELLDPEKEKDHLLVPTGKFDGLPTAIQAIGIGGVGLTIWLIITSFMMIGALYFFPDVLALDLLKYPVVNLSVPGVDIP GLNDIP A0A0G4GX86 Photosystem I protein (PsaI) Chromera velia RM12 0.022553562 1 LEVO MQVVSVFAAVALAASSASAFVPSTSRSSGLLSKQRKTELNALEDAFFAPVEELMNAAPASVDFSDAISSSSEVLASIAAD SKLAVDVQGELVPAMIAAAEKLAANPGAKAGEILDPNSKLVQLRQVGGLVTGRHGVTNFDNKVPFLLLGAAPALFHTFLF FGLATVFVFKQENETPFRRQYGGTGYPRLDPYTMHRGDKPRERDWNDPITM A0A0G4HFQ7 Photosystem I reaction center subunit V Chromera velia RM12 0.029700710999999998 1 LEVO MKVALGFLASFVCGSAARDTGFLSPAQRLASSGSRRKASSPVDPVSSLFDASTSEPGKVSKFAGWSPTLSEMPSAWEGYS VLRDSDASRTLLTKIPVYRRGLPPSWAGLEVGMAHGYLFFGPFAFLGPLRDSEEFWALAGLAASSGFDMILTIGLTVYGA YQDKWKLCNPCDKWITRNYSGGFDVKPSPDLTPIGNALVSGPGNNGFFLSDPRSPNSMYEDFQKFTTMFLIGALGGSLFA YYLCATTHAFDPVGGIRTFLGVPAITGYEPPPQAIIP A0A0G4GX71 Photosystem I protein (PsaM) Chromera velia RM12 0.022135116999999996 1 LEVO MKFLSASLLGCFVTSSAFVLQAPRSLRPASPVRRLENPRPVETVTNAFDFSQIDTGVLNVSADPDLYQSIRLFTLIAVFA ITLGSVARRFSPSINDYQVDQDYIELKRKNYFPSEDEFLDNRKDFESQTKKTTEMFEACKTWGAYAALRNSGAGKKKAQE FLGIKSDAELKAIENKAELMKWYGSYKSNERKVAW Photosystem I protein (PsaR) Chromera velia RM12 0.022594372999999997 1 LEVO MPSIRLVATAVAVGMGVTSAFQQTPIRALKQRSEASTTLNDVKEMDLDSTWTYVKNRNIKPITEAKKLDILRTQILPVGT EQHAEAVHEILRNADLPMGVAQTNAVKRAPANVVLAGAVILFLIGFLGHWMNVINVPRGLPLLFGWPRVSWLAISSLMLP AYFLHLEGYNTIQRDAMYEELAKYGIKREDPFLEPPRELIKP A0A0G4FDJ8 Plastid light harvesting protein Chromera velia RM12 0.032446844 1 LEVO MVSLTRAGLAVGCVAVATVSAGRPAFLSSAPLQAMRARENHTARDGKIQLTPEDAGVVRKHGITVAPGFPLIGDSEPFGF FDPLGLSAGKNPEQVAKLREAELKHCRIAMLAVLGWFSVVNNFYFFYGGELGTDPIEAWQKVNLAGKAQILLFIGLLEWF TIAIKEYQKTTPGRLCIPGDYFGAYGWLVDETQTRYGENLDSFNKYDWEVEEFGRGNALQFLTVDEWVDYQTQELNNGRL AMVAIAGLFIQDVLFKQPGDLIFKPYFDTTVQFFNDLISDTHTAEGMINAGLL A0A0G4ID45 Plastid light harvesting protein Chromera velia RM12 0.026235361 1 LEVO MKRLAFLAFASGVTAFQPLKPSSAPTSARDAVTSLRQEVVQEVRMSQALPFLPQPQDLNGEMAGDVGFDPLGFSSYYRDP QNPSWFKLEYFREAEVKHGRIAMLAALGALHVELLGPVPIDPFIKITEKSAYDAFCHLLVTNPVYFWATLIALHAIEVTS LGATAFMMTNPDAQREPGDYNLRFFGYDKLSPEKKKDLQTKEIKNGRLAMIAMIGMLHMNRVTGLGAIELLGKALNG A0A0G4FL36 Plastid light harvesting protein Chromera velia RM12 0.024313141 1 LEVO MKSILCVAALAVTGTLPVSEAFTPLLATKAPSRAEATSRKAVADMVGVDTDSGNTVWDPLDIASKCEFNRKKGRDNVIFS TWPHLNWMREAELKHGRICMLAVLGVLFTKLGIKIGGFISNSSTDWWENLGRVWAEHPEVIAFIIMAGGFIDMATYDTRM WSGNNKREAGNLGFDPLNLMAKDDNFALKELKHGRLAMVAMAAFAAERGIDTSVPLLHLAGF A0A0G4HNB1 Plastid light harvesting protein Chromera velia RM12 0.024079018 1 LEVO MKRVAAVTGVIALAGCANAFVPPTSPVVSTRTASEGRTVARMEKSESLPFLRRPEGEIFKEKWAGDKGFDPLFLSEYYDL PTMKIFREAELKHGRVAMMAFLGLLLQNILRLPGAPSEANPVYALFKTNPQWVALLFITVGILENIGYKGEMDSIIWFKG KLKDRKPGDMGAEKLDFLNLAQKENAEAQEVEHCRAAMVGTIGLLLQYIASGREQPF A0A0G4HMN0 Chlorophyll a-b binding protein, chloroplastic Chromera velia RM12 0.031759348 1 LEVO MRVLAGLLCASASAVAVNAYIDYGGGVDYRPDERKALQRRTLIDRDLYKERKQVVIGKIYDLNDLPGASNENQFFIGSEA NKPWDPLGLTRKAREREGGVFNYWLEPIQRDLKTAYKTDNDVGFGLEYVDYVFDPLWWFRESELVHCRVCMLAFAGWMAT ELGFRLPYEAFQGVSALEAHDALVKSGHMQLMLHFIVFLEFLRHRRFLAMRKGDLGTASNIEPGDYGFDPLGFKQKPEYR KYQTNELKNGRLAMIAMSAILTQAALDPTSKFPNYLF A0A0G4I0G6 Photosystem I protein (PsaV) Chromera velia RM12 0.045973148 1 LEVO MVRGGLSTVVSAALVGCAVAFTGTPLKPPSSDTSLSAVKKSSKKFGDLSQFTGDVKGDAEAYRQILYATTGDPKYKKAKK SVGLIKWMKQMDPNEFKLKFIVVPGLLTVAAAGAFVALSNLDLPTLPSTPSPEDAGKFFLTIPAVGTIRAKPLLGDSGAF LPGSEPAPKITSKAEQVAIQKKIKAKITPAAKEAAKKLSLPKPGAKMSGGFVQRFIDASPERKDPGLDLIKDSVSDASKF SAPTQTLNVAGSIDSLLAKANLPSVDLTFSPAVEPAYALWEGGGKSTDPAYPGRAGFDEFKKEQMKIAAKTPTMTYFGES IKGDPRPGLKTYGMPQEYIDRMRKNTQWMKDRGVVFYPGYKEGSINREWTKLIKRSPTVEEQKKFISQHPEYLYNVQIPG MDDAKAIQKIQPKMEPKVWRRVGP A0A0G4HRT4 Photosystem I P700 chlorophyll a apoprotein A1 Chromera velia RM12 0.029865294999999997 1 LEVO QPLRLSNTAKMPMSTTWIWNLHSDSNESVGSILKDSQVRFEFVQIAQLIVIALWLVNNIRQIATFSNVVAWSINPLDTRP TLGNTQGFVGEAILNRTSDAFQGGGIQMTSGVVELLRGEGYLAPPDAASAALGLLMGLLIIITISGRKLNLTLNWSQGLI LTGGALVAWAGHLALVAIPAQSIWATLELDRSGVLLGWGQPQLISLVCFQNGITVLNGGAVALDTQVIHHLALALVILAP LALAPLIVRGSDGNDILLVENTDAHLPGLEESSDNKDIDY Photosystem I protein (PsaB) Chromera velia RM12 0.128908375 1 LEVO MWSLEQMRDEVYEFSKKGFRKTFNLVVSEPSHTAIMPKENSILTFRFTDGEEVPPSDGRLGEVSPHNGEEAKISRDHVQA NLRIEQTRVGSRYVLSVSPLSNPTGDKDSHHHQFWLPEELVKKITFFRDKEDSVGITIAAIPPKDYLESRLYSKTESEVP SPDGQEGEVPPQAEAKFRIIKTTEGPYSVLKAYPPNQVNPGTFRLPSFLLGNRDFQVGLNEKNEPFLDMFLYTPILVIWG SLGGKLPPQEWEVGGWSWDYVPQVLWPNSRTRFVLTNEGPNQLTILVGSQQGPKSEPTTKDPKSDPDKKKDGPWFRKSKG KDITVTSELSTTQRLWNRLSQVNDFPSTMPEGNVIVQIFRSHLVQLALILFWAAGILTLSTYQGNFTQWELLPTKIRPVA HQIWDPHFGDALSRIYSDFWSNKTVGEGASSTWSSLNYLTCGLFNWWFTIGFRSTEDLLNAALGCFLGGIFLLVLQILGP VSPEWPTPVSQWTSKSVLSLGFSRELWGEIPGFDVKEDANDSDMEANLSPNWSLSVQGLIWTNQLFLGSFKLFNLSSAYL SFALIAPLFKYFINLYFLKDLLYFAGCGSLSWSGHLIHIAIPESRGIHVRGDNLLTTLPHPNGIVPLLTGDLQAYAQAPD SSTHVFGTPVGSGTAMLTFSGNIYQNTSQIFPLTDVAHHHLAIGVLFLIIDGTLRILNLGNLGLLFSSANRYSAFQMWNS NTGEFIQSIIYMFSSSLHFRLAVNLSVFSTLSSLTAQHIYALPVYAYLNQDFLSQAALYVHHQYIAGLLIMGGFVHGTLF LIYDYQQNSIWDRIFFSAVFKFLDNKLNIILWLSWITFFLGFHTLGLYVHNDVVTAFGHSERQILLQPVFAQLIQTASGK NIYYPDFVKLFYPLNQRDPRFLNGWLETINNLKVSPFLNVGPGDFLVHHAIALGLHTTVLILIKGAIDSRGSRFMPDKQA FGYTFPCDGPGRGGTCDISAWDSFYLAMFWMLNTIGWVTFYWHWKHLALWGGTNRLFDESSVCLMGWLRDYLWLNSSKLI YGYTSETVSINSVWAWAFLLGHLVWATGFMFLISWRGYWQELIETLVWAHERTPIANLFQWADTPVALSILQARFVGLVH FTVGYILTYAAFLLASTPV D9IXI4 1.97.1.12 FE (III) ION 5.5845e-05 1 FE CHLOROPHYLL A 0.000893489 114 CLA CHLOROPHYLL A ISOMER 0.000893489 1 CL0 IRON/SULFUR CLUSTER 0.00035163999999999996 3 SF4 PHYLLOQUINONE 0.000450696 2 PQN (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL 0.00060087 22 XAT 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE 0.0007871579999999999 11 LMG DIGALACTOSYL DIACYL GLYCEROL (DGDG) 0.0009492989999999999 6 DGD DODECYL-BETA-D-MALTOSIDE 0.000510615 71 LMT BETA-CAROTENE 0.000536873 8 BCR Lauryl Maltose Neopentyl Glycol 0.001005188 1 AV0 [(1~{R},5~{S})-3,3,5-trimethyl-5-oxidanyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{Z})-3,7,12,16-tetramethyl-17-oxidanyl-19-oxidanylidene-19-[(1~{R},4~{S})-1,2,2-trimethyl-4-oxidanyl-cyclopentyl]nonadeca-1,3,5,7,9,11,13,15,17-nonaenylidene]cyclohexyl] ethanoate 0.0006589059999999999 4 A1L6D 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL 0.0007951159999999999 1 SQD [(2~{R})-3-[(2~{S},3~{R},4~{R},5~{R},6~{R})-6-(hexadecanoyloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-octadecanoyloxy-propyl] octadecanoate 0.001025567 1 A1I05 water 1.8015e-05 1558 HOH singleParticle particle 0.8 6.5 20.0 C6H13NO4S MES

20 mM MES pH 6.5, 0.15M NaCl and 0.01% Lauryl maltose neopentyl glycol

Quantifoil COPPER 300 GLOW DISCHARGE 45 OTHER

GloQube Plus instrument (Quorum Technologies, UK) was used for glow discharge with the currency of 35 mA For the sample from Gel, glow discharge time is 30, waiting time is 5 sec and blowing time is 3 seconds

ETHANE 100 277

Blotting time 2.5 sec..

Protein sample in buffer solution of 20 mM MES pH 6.5, 0.15M NaCl and 0.01% Lauryl maltose neopentyl glycol

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.8 2.1 165000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 79.0 81.0 TFS Selectris X 10 FEI FALCON IV (4k x 4k) 2 32897 3.16 40.0

Two dataset were collected and merged together during data processing.

Motion correction and CTF estimation were performed on the raw data in cryoSPARC's Live session

5807142

Blob picking was selected initially.

CTF estimation were performed on the raw data in cryoSPARC's Live session

PHASE FLIPPING AND AMPLITUDE CORRECTION Ab initio reconstruction was used to create initial models for both datasets.

Data for Ab initio reconstruction were obtained from the dataset after two rounds 2d classification.

C1 BACK PROJECTION 1.84 FSC 0.143 CUT-OFF RELION

The particles from both datasets were converted into star files using csparc2star from the PyEM suite for further processing in RELION v5.0.0b.

532822 ANGULAR RECONSTITUTION ANGULAR RECONSTITUTION 5

For Dataset 1, two rounds of heterogeneous refinement were performed using five classes. Dataset 2 underwent eight rounds of heterogeneous refinement using five classes.

emd_52518.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 500 500 500 0 0 0 500 500 500 364.5 364.5 364.5 90.0 90.0 90.0 X Y Z -48.502727999999998 153.802799999999991 0.015173205 1.246312 0.729 0.729 0.729 8.0 AUTHOR ::::EMDATABANK.org::::EMD-52518:::: SwissModel in silico model RIGID BODY FIT CCC in ChimeraX REAL 21.600000000000001