EMDB-52518: Cryo-EM structure of the Chromera velia PSI supercomplex at 1.84 ...

Basic information

Entry

Database: EMDB / ID: EMD-52518

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

Sample

• Complex: PSI super complex from Chrome velia
  • Protein or peptide: x 18 types
• Protein or peptide: x 1 types
• Ligand: x 15 types

• Keywords: Photosynthesis / Photosystem I / PSI-FCP complex / Chrome velia / Cryo-EM.

Function / homology

Function:

thylakoid membrane / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / superoxide dismutase / chlorophyll binding / superoxide dismutase activity / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / metal ion binding / membrane

Domain/homology:

Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I protein PsaC / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / : / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Prokaryotic membrane lipoprotein lipid attachment site profile.

Component:

Superoxide dismutase [Fe] / Uncharacterized protein / Uncharacterized protein / PSI subunit V / Photosystem I reaction center subunit III / Uncharacterized protein / Photosystem I reaction center subunit II / Uncharacterized protein / Superoxide dismutase [Fe] / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Chlorophyll a-b binding protein, chloroplastic / Plastid light harvesting protein / Photosystem I iron-sulfur center / photosystem I / photosystem I

• Biological species: Chromera velia (eukaryote)
• Method: single particle reconstruction / cryo EM / Resolution: 1.84 Å
• Authors: Yuan X / Qian P / Sobotka R / Naschberger A

Funding support

European Union, 1 items

Organization	Grant number	Country
European Research Council (ERC)	Synergy Award 854126	European Union

• Citation: Journal: To Be Published; Title: Cryo-EM structure of PSI super complex from Chromera. velia; Authors: Yuan X / Qian P / Sobotka R / Naschberger A

History

Deposition	Jan 10, 2025	-
Header (metadata) release	Jan 28, 2026	-
Map release	Jan 28, 2026	-
Update	Jan 28, 2026	-
Current status	Jan 28, 2026	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_52518.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 0.729 Å

Density

Contour Level	By AUTHOR: 8.0
Minimum - Maximum	-48.502727999999998 - 153.802799999999991
Average (Standard dev.)	0.015173205 (±1.246312)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 500 500 500 Spacing 500 500 500
Cell	A=B=C: 364.5 Å α=β=γ: 90.0 °

Supplemental data

Sample components

Entire : PSI super complex from Chrome velia

• Entire: Name: PSI super complex from Chrome velia

Components

• Complex: PSI super complex from Chrome velia
  • Protein or peptide: Superoxide dismutase [Fe]
  • Protein or peptide: Superoxide dismutase [Fe]
  • Protein or peptide: Photosystem I protein (PsaI)
  • Protein or peptide: photosystem I
  • Protein or peptide: Photosystem I iron-sulfur center
  • Protein or peptide: Photosystem I reaction center subunit II
  • Protein or peptide: Photosystem I reaction center subunit IV
  • Protein or peptide: Photosystem I reaction center subunit III
  • Protein or peptide: Photosystem I reaction center subunit V
  • Protein or peptide: Photosystem I protein (PsaM)
  • Protein or peptide: Photosystem I protein (PsaR)
  • Protein or peptide: Plastid light harvesting protein
  • Protein or peptide: Plastid light harvesting protein
  • Protein or peptide: Plastid light harvesting protein
  • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Protein or peptide: Photosystem I protein (PsaV)
  • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A1
  • Protein or peptide: Photosystem I protein (PsaB)
• Protein or peptide: Plastid light harvesting protein
• Ligand: FE (III) ION
• Ligand: CHLOROPHYLL A
• Ligand: CHLOROPHYLL A ISOMER
• Ligand: IRON/SULFUR CLUSTER
• Ligand: PHYLLOQUINONE
• Ligand: (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
• Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
• Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
• Ligand: DODECYL-BETA-D-MALTOSIDE
• Ligand: BETA-CAROTENE
• Ligand: Lauryl Maltose Neopentyl Glycol
• Ligand: [(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
• Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
• Ligand: [(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
• Ligand: water

Supramolecule #1: PSI super complex from Chrome velia

• Supramolecule: Name: PSI super complex from Chrome velia / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2, #8, #3-#7, #9-#13, #15-#19; Details: A complex containing PSI as a core with other components for example PsaA-, PsaB, Psa
• Source (natural): Organism: Chromera velia (eukaryote) / Strain: RM12
• Molecular weight: Theoretical: 654.4 KDa

Macromolecule #1: Superoxide dismutase [Fe]

• Macromolecule: Name: Superoxide dismutase [Fe] / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: superoxide dismutase
• Source (natural): Organism: Chromera velia (eukaryote) / Strain: RM12
• Molecular weight: Theoretical: 41.899281 KDa

Sequence

String:

MRVHPVVAVS GLGVSAVSAF VFRGTPSAGI PRASPAATEL SNYPERVAKE PGWAKVEYEI GGIGWSNPAI DEANENITKK MQANGETIF NLWAPWDQAQ VRTQDAPSYR ELMDVVDFTW QIPGTERWWY DLNIDDAVRM QPFPLERIRF DPRNLQPHRF P EQVFDHLA EYHAPYVRKL KALVEGTPLE KESLEELASR KTRNETIDNA VGMCYNTGLY WESLSSKSDW GGDQWAHGPL KE KIEKKYG SLKGFKDAVV TAGMALFGSG HLWIVSDKTG EVDIVTTSDA SNPMREGKGY PLLVCDLWEH AFYEDFRNDK KKA LTSWLN LMNWQKGNKR LETYMEKMKL KDLAPTPAQE MKPKEPEPTP GPAA

UniProtKB: Superoxide dismutase [Fe]

Macromolecule #2: Superoxide dismutase [Fe]

• Macromolecule: Name: Superoxide dismutase [Fe] / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: superoxide dismutase
• Source (natural): Organism: Chromera velia (eukaryote) / Strain: RM12
• Molecular weight: Theoretical: 29.93184 KDa

Sequence

String:

MRFATLSLLG FFGASEAIRS RDLQAFVVSA PGASSPSRRS PATALDAVAV GSNVYEKMGV STLVSGEEGP FKLKELPWFP TVLAPMMSY ETISYHYGKH HALYVRNLNA LAKEDSSLAS KSLEDIFKGA EKGKKLFNQA AQVWNHDFFW NSMSPEGGDE S FSETSKVK SAIISQWEDL GKFKEEWVKL ALKHFGSGWI WLVQQKDGKL AIVDTHNAMN PISENLGTPL MTMDIWEHAY YV DHKSNKG LYTASFFEVC NWDFAEKNME

UniProtKB: Superoxide dismutase [Fe]

Macromolecule #3: photosystem I

• Macromolecule: Name: photosystem I / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
• Source (natural): Organism: Chromera velia (eukaryote) / Strain: RM12
• Molecular weight: Theoretical: 44.801406 KDa

Sequence

String:

MPLNGLLAVQ LWFFGTVSIL VAHVMFAFPP YPFLAQNYAT QISLFTHHMW IGGFLLVGSG AHASLYLIRE QGDLTRTNSL VALCLNYRD AIISHLNWLC IFLGLHSFGI YIHNDTLAAL GRFDDQITNL PPLGAEWFQH AVTANFPINN GFKNHFNTQI L MNDKIVFS NLSFNTADFL VHHIHAFTIH VTVLILVKGI LFSRDSNLIS DKYALGFRFP CDGPGRGGTC QVSGWDHIFL AL FWMYNSI SVVIFHFFWK VQSDVWGYQS LDNGITHITN GNFTKSALTI NGWLRDFLWA EAAQVVQSYS TPFFVYGLVF LGA HFIWAF SLMFLFSGRG YWQELIDYYT YAVYKWSQLP YLAFQALSIV QGRAVGLAHY LLGGIGTTWA FFLARALTL

UniProtKB: photosystem I

Macromolecule #4: Photosystem I iron-sulfur center

• Macromolecule: Name: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
• Source (natural): Organism: Chromera velia (eukaryote) / Strain: RM12
• Molecular weight: Theoretical: 8.961316 KDa

Sequence

String:

MHNVGIYTTC IGCTQCVRAC PTEVLDMMTW DHCRAQQIAC SDTLQDCIGC KRCETACPTD FLSIRVELGT ENYYSMGLAY

UniProtKB: Photosystem I iron-sulfur center

Macromolecule #5: Photosystem I reaction center subunit II

• Macromolecule: Name: Photosystem I reaction center subunit II / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chromera velia (eukaryote) / Strain: RM12
• Molecular weight: Theoretical: 30.636371 KDa

Sequence

String:

MKFLAVAALI CVGGARAFVA PSAPSNRQLA TELRAGVPAN PKPGSQFDLS VPDKDTLIRR RGGRGWLGKA NNYGRFLISW THNKAEPFP CPTGGSSLMK PGANRLLLAK KEQGIALGRW LKRTLKIDNW KIFEIKPDGT VIFRSPKDGI YPEKKDPERV K RLTLLGSS YDNQERMARY SARKQFRSYE KYLKEQGEMA TWQYILQRFR AESIQAFDAD FGDMDVQEAQ REGYAKMRAE KQ KEMGEGV ISPAMIQMYM QILKDPYKGR RD

UniProtKB: Photosystem I reaction center subunit II

Macromolecule #6: Photosystem I reaction center subunit IV

• Macromolecule: Name: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chromera velia (eukaryote) / Strain: RM12
• Molecular weight: Theoretical: 14.430821 KDa

Sequence

String:

MKLASALLLL CLSATCAFAR RLSGFLSGLP SRQRDGARQA TVLEAIQKGS KVLILKPESY FYGFTGDVVV VDKNPFYPYG VTVKFPSMQ YKGLNTFNFK LDELQEVAPP APKKKKKKAA VNPAAEPAEP AASS

UniProtKB: Uncharacterized protein

Macromolecule #7: Photosystem I reaction center subunit III

• Macromolecule: Name: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chromera velia (eukaryote) / Strain: RM12
• Molecular weight: Theoretical: 35.865297 KDa

Sequence

String:

MRVSLCMAIG AASVASEASA FVAPPSRMGR GLLSSQLRAE RPSKTEASEA RSKEFDESIF DQAMLEDDDS AFDPMMDFAR LATPAAIAM AAATVAPQVA HAADATLVPC AESKRFQTIM KAEIKANEKR VKENPKGSFF RDQFIAELKR SKIRKWRFEH S SLMCSKED GKPRVDVTNP NQIFGGFFAF VYVLGAIGWS AKTYNRGIKA AYGPDGGWKE VILDWPFVLQ VFYHSLGWPG RT WKELLDP EKEKDHLLVP TGKFDGLPTA IQAIGIGGVG LTIWLIITSF MMIGALYFFP DVLALDLLKY PVVNLSVPGV DIP GLNDIP

UniProtKB: Photosystem I reaction center subunit III

Macromolecule #8: Photosystem I protein (PsaI)

• Macromolecule: Name: Photosystem I protein (PsaI) / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chromera velia (eukaryote) / Strain: RM12
• Molecular weight: Theoretical: 22.553562 KDa

Sequence

String:

MQVVSVFAAV ALAASSASAF VPSTSRSSGL LSKQRKTELN ALEDAFFAPV EELMNAAPAS VDFSDAISSS SEVLASIAAD SKLAVDVQG ELVPAMIAAA EKLAANPGAK AGEILDPNSK LVQLRQVGGL VTGRHGVTNF DNKVPFLLLG AAPALFHTFL F FGLATVFV FKQENETPFR RQYGGTGYPR LDPYTMHRGD KPRERDWNDP ITM

UniProtKB: Uncharacterized protein

Macromolecule #9: Photosystem I reaction center subunit V

• Macromolecule: Name: Photosystem I reaction center subunit V / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chromera velia (eukaryote) / Strain: RM12
• Molecular weight: Theoretical: 29.700711 KDa

Sequence

String:

MKVALGFLAS FVCGSAARDT GFLSPAQRLA SSGSRRKASS PVDPVSSLFD ASTSEPGKVS KFAGWSPTLS EMPSAWEGYS VLRDSDASR TLLTKIPVYR RGLPPSWAGL EVGMAHGYLF FGPFAFLGPL RDSEEFWALA GLAASSGFDM ILTIGLTVYG A YQDKWKLC NPCDKWITRN YSGGFDVKPS PDLTPIGNAL VSGPGNNGFF LSDPRSPNSM YEDFQKFTTM FLIGALGGSL FA YYLCATT HAFDPVGGIR TFLGVPAITG YEPPPQAIIP

UniProtKB: PSI subunit V

Macromolecule #10: Photosystem I protein (PsaM)

• Macromolecule: Name: Photosystem I protein (PsaM) / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chromera velia (eukaryote) / Strain: RM12
• Molecular weight: Theoretical: 22.135117 KDa

Sequence

String:

MKFLSASLLG CFVTSSAFVL QAPRSLRPAS PVRRLENPRP VETVTNAFDF SQIDTGVLNV SADPDLYQSI RLFTLIAVFA ITLGSVARR FSPSINDYQV DQDYIELKRK NYFPSEDEFL DNRKDFESQT KKTTEMFEAC KTWGAYAALR NSGAGKKKAQ E FLGIKSDA ELKAIENKAE LMKWYGSYKS NERKVAW

Macromolecule #11: Photosystem I protein (PsaR)

• Macromolecule: Name: Photosystem I protein (PsaR) / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chromera velia (eukaryote) / Strain: RM12
• Molecular weight: Theoretical: 22.594373 KDa

Sequence

String:

MPSIRLVATA VAVGMGVTSA FQQTPIRALK QRSEASTTLN DVKEMDLDST WTYVKNRNIK PITEAKKLDI LRTQILPVGT EQHAEAVHE ILRNADLPMG VAQTNAVKRA PANVVLAGAV ILFLIGFLGH WMNVINVPRG LPLLFGWPRV SWLAISSLML P AYFLHLEG YNTIQRDAMY EELAKYGIKR EDPFLEPPRE LIKP

UniProtKB: Uncharacterized protein

Macromolecule #12: Plastid light harvesting protein

• Macromolecule: Name: Plastid light harvesting protein / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chromera velia (eukaryote) / Strain: RM12
• Molecular weight: Theoretical: 32.446844 KDa

Sequence

String:

MVSLTRAGLA VGCVAVATVS AGRPAFLSSA PLQAMRAREN HTARDGKIQL TPEDAGVVRK HGITVAPGFP LIGDSEPFGF FDPLGLSAG KNPEQVAKLR EAELKHCRIA MLAVLGWFSV VNNFYFFYGG ELGTDPIEAW QKVNLAGKAQ ILLFIGLLEW F TIAIKEYQ KTTPGRLCIP GDYFGAYGWL VDETQTRYGE NLDSFNKYDW EVEEFGRGNA LQFLTVDEWV DYQTQELNNG RL AMVAIAG LFIQDVLFKQ PGDLIFKPYF DTTVQFFNDL ISDTHTAEGM INAGLL

UniProtKB: Plastid light harvesting protein

Macromolecule #13: Plastid light harvesting protein

• Macromolecule: Name: Plastid light harvesting protein / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chromera velia (eukaryote) / Strain: RM12
• Molecular weight: Theoretical: 26.235361 KDa

Sequence

String:

MKRLAFLAFA SGVTAFQPLK PSSAPTSARD AVTSLRQEVV QEVRMSQALP FLPQPQDLNG EMAGDVGFDP LGFSSYYRDP QNPSWFKLE YFREAEVKHG RIAMLAALGA LHVELLGPVP IDPFIKITEK SAYDAFCHLL VTNPVYFWAT LIALHAIEVT S LGATAFMM TNPDAQREPG DYNLRFFGYD KLSPEKKKDL QTKEIKNGRL AMIAMIGMLH MNRVTGLGAI ELLGKALNG

UniProtKB: Uncharacterized protein

Macromolecule #14: Plastid light harvesting protein

• Macromolecule: Name: Plastid light harvesting protein / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chromera velia (eukaryote) / Strain: RM12
• Molecular weight: Theoretical: 24.313141 KDa

Sequence

String:

MKSILCVAAL AVTGTLPVSE AFTPLLATKA PSRAEATSRK AVADMVGVDT DSGNTVWDPL DIASKCEFNR KKGRDNVIFS TWPHLNWMR EAELKHGRIC MLAVLGVLFT KLGIKIGGFI SNSSTDWWEN LGRVWAEHPE VIAFIIMAGG FIDMATYDTR M WSGNNKRE AGNLGFDPLN LMAKDDNFAL KELKHGRLAM VAMAAFAAER GIDTSVPLLH LAGF

UniProtKB: Uncharacterized protein

Macromolecule #15: Plastid light harvesting protein

• Macromolecule: Name: Plastid light harvesting protein / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chromera velia (eukaryote) / Strain: RM12
• Molecular weight: Theoretical: 24.079018 KDa

Sequence

String:

MKRVAAVTGV IALAGCANAF VPPTSPVVST RTASEGRTVA RMEKSESLPF LRRPEGEIFK EKWAGDKGFD PLFLSEYYDL PTMKIFREA ELKHGRVAMM AFLGLLLQNI LRLPGAPSEA NPVYALFKTN PQWVALLFIT VGILENIGYK GEMDSIIWFK G KLKDRKPG DMGAEKLDFL NLAQKENAEA QEVEHCRAAM VGTIGLLLQY IASGREQPF

UniProtKB: Uncharacterized protein

Macromolecule #16: Chlorophyll a-b binding protein, chloroplastic

• Macromolecule: Name: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chromera velia (eukaryote) / Strain: RM12
• Molecular weight: Theoretical: 31.759348 KDa

Sequence

String:

MRVLAGLLCA SASAVAVNAY IDYGGGVDYR PDERKALQRR TLIDRDLYKE RKQVVIGKIY DLNDLPGASN ENQFFIGSEA NKPWDPLGL TRKAREREGG VFNYWLEPIQ RDLKTAYKTD NDVGFGLEYV DYVFDPLWWF RESELVHCRV CMLAFAGWMA T ELGFRLPY EAFQGVSALE AHDALVKSGH MQLMLHFIVF LEFLRHRRFL AMRKGDLGTA SNIEPGDYGF DPLGFKQKPE YR KYQTNEL KNGRLAMIAM SAILTQAALD PTSKFPNYLF

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

Macromolecule #17: Photosystem I protein (PsaV)

• Macromolecule: Name: Photosystem I protein (PsaV) / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chromera velia (eukaryote) / Strain: RM12
• Molecular weight: Theoretical: 45.973148 KDa

Sequence

String:

MVRGGLSTVV SAALVGCAVA FTGTPLKPPS SDTSLSAVKK SSKKFGDLSQ FTGDVKGDAE AYRQILYATT GDPKYKKAKK SVGLIKWMK QMDPNEFKLK FIVVPGLLTV AAAGAFVALS NLDLPTLPST PSPEDAGKFF LTIPAVGTIR AKPLLGDSGA F LPGSEPAP KITSKAEQVA IQKKIKAKIT PAAKEAAKKL SLPKPGAKMS GGFVQRFIDA SPERKDPGLD LIKDSVSDAS KF SAPTQTL NVAGSIDSLL AKANLPSVDL TFSPAVEPAY ALWEGGGKST DPAYPGRAGF DEFKKEQMKI AAKTPTMTYF GES IKGDPR PGLKTYGMPQ EYIDRMRKNT QWMKDRGVVF YPGYKEGSIN REWTKLIKRS PTVEEQKKFI SQHPEYLYNV QIPG MDDAK AIQKIQPKME PKVWRRVGP

UniProtKB: Uncharacterized protein

Macromolecule #18: Photosystem I P700 chlorophyll a apoprotein A1

• Macromolecule: Name: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chromera velia (eukaryote) / Strain: RM12
• Molecular weight: Theoretical: 29.865295 KDa

Sequence

String:

QPLRLSNTAK MPMSTTWIWN LHSDSNESVG SILKDSQVRF EFVQIAQLIV IALWLVNNIR QIATFSNVVA WSINPLDTRP TLGNTQGFV GEAILNRTSD AFQGGGIQMT SGVVELLRGE GYLAPPDAAS AALGLLMGLL IIITISGRKL NLTLNWSQGL I LTGGALVA WAGHLALVAI PAQSIWATLE LDRSGVLLGW GQPQLISLVC FQNGITVLNG GAVALDTQVI HHLALALVIL AP LALAPLI VRGSDGNDIL LVENTDAHLP GLEESSDNKD IDY

Macromolecule #19: Photosystem I protein (PsaB)

• Macromolecule: Name: Photosystem I protein (PsaB) / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
• Source (natural): Organism: Chromera velia (eukaryote) / Strain: RM12
• Molecular weight: Theoretical: 128.908375 KDa

Sequence

String:

MWSLEQMRDE VYEFSKKGFR KTFNLVVSEP SHTAIMPKEN SILTFRFTDG EEVPPSDGRL GEVSPHNGEE AKISRDHVQA NLRIEQTRV GSRYVLSVSP LSNPTGDKDS HHHQFWLPEE LVKKITFFRD KEDSVGITIA AIPPKDYLES RLYSKTESEV P SPDGQEGE VPPQAEAKFR IIKTTEGPYS VLKAYPPNQV NPGTFRLPSF LLGNRDFQVG LNEKNEPFLD MFLYTPILVI WG SLGGKLP PQEWEVGGWS WDYVPQVLWP NSRTRFVLTN EGPNQLTILV GSQQGPKSEP TTKDPKSDPD KKKDGPWFRK SKG KDITVT SELSTTQRLW NRLSQVNDFP STMPEGNVIV QIFRSHLVQL ALILFWAAGI LTLSTYQGNF TQWELLPTKI RPVA HQIWD PHFGDALSRI YSDFWSNKTV GEGASSTWSS LNYLTCGLFN WWFTIGFRST EDLLNAALGC FLGGIFLLVL QILGP VSPE WPTPVSQWTS KSVLSLGFSR ELWGEIPGFD VKEDANDSDM EANLSPNWSL SVQGLIWTNQ LFLGSFKLFN LSSAYL SFA LIAPLFKYFI NLYFLKDLLY FAGCGSLSWS GHLIHIAIPE SRGIHVRGDN LLTTLPHPNG IVPLLTGDLQ AYAQAPD SS THVFGTPVGS GTAMLTFSGN IYQNTSQIFP LTDVAHHHLA IGVLFLIIDG TLRILNLGNL GLLFSSANRY SAFQMWNS N TGEFIQSIIY MFSSSLHFRL AVNLSVFSTL SSLTAQHIYA LPVYAYLNQD FLSQAALYVH HQYIAGLLIM GGFVHGTLF LIYDYQQNSI WDRIFFSAVF KFLDNKLNII LWLSWITFFL GFHTLGLYVH NDVVTAFGHS ERQILLQPVF AQLIQTASGK NIYYPDFVK LFYPLNQRDP RFLNGWLETI NNLKVSPFLN VGPGDFLVHH AIALGLHTTV LILIKGAIDS RGSRFMPDKQ A FGYTFPCD GPGRGGTCDI SAWDSFYLAM FWMLNTIGWV TFYWHWKHLA LWGGTNRLFD ESSVCLMGWL RDYLWLNSSK LI YGYTSET VSINSVWAWA FLLGHLVWAT GFMFLISWRG YWQELIETLV WAHERTPIAN LFQWADTPVA LSILQARFVG LVH FTVGYI LTYAAFLLAS TPV

UniProtKB: photosystem I

Macromolecule #22: FE (III) ION

• Macromolecule: Name: FE (III) ION / type: ligand / ID: 22 / Number of copies: 1 / Formula: FE
• Molecular weight: Theoretical: 55.845 Da

Macromolecule #23: CHLOROPHYLL A

• Macromolecule: Name: CHLOROPHYLL A / type: ligand / ID: 23 / Number of copies: 114 / Formula: CLA
• Molecular weight: Theoretical: 893.489 Da

Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

Macromolecule #24: CHLOROPHYLL A ISOMER

• Macromolecule: Name: CHLOROPHYLL A ISOMER / type: ligand / ID: 24 / Number of copies: 1 / Formula: CL0
• Molecular weight: Theoretical: 893.489 Da

Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

Macromolecule #25: IRON/SULFUR CLUSTER

• Macromolecule: Name: IRON/SULFUR CLUSTER / type: ligand / ID: 25 / Number of copies: 3 / Formula: SF4
• Molecular weight: Theoretical: 351.64 Da

Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

Macromolecule #26: PHYLLOQUINONE

• Macromolecule: Name: PHYLLOQUINONE / type: ligand / ID: 26 / Number of copies: 2 / Formula: PQN
• Molecular weight: Theoretical: 450.696 Da

Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

Macromolecule #27: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...

• Macromolecule: Name: (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; type: ligand / ID: 27 / Number of copies: 22 / Formula: XAT
• Molecular weight: Theoretical: 600.87 Da

Chemical component information

ChemComp-XAT:
(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

Macromolecule #28: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

• Macromolecule: Name: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 28 / Number of copies: 11 / Formula: LMG
• Molecular weight: Theoretical: 787.158 Da

Chemical component information

ChemComp-LMG:
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

Macromolecule #29: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

• Macromolecule: Name: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 29 / Number of copies: 6 / Formula: DGD
• Molecular weight: Theoretical: 949.299 Da

Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

Macromolecule #30: DODECYL-BETA-D-MALTOSIDE

• Macromolecule: Name: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 30 / Number of copies: 71 / Formula: LMT
• Molecular weight: Theoretical: 510.615 Da

Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

Macromolecule #31: BETA-CAROTENE

• Macromolecule: Name: BETA-CAROTENE / type: ligand / ID: 31 / Number of copies: 8 / Formula: BCR
• Molecular weight: Theoretical: 536.873 Da

Chemical component information

ChemComp-BCR:
BETA-CAROTENE

Macromolecule #32: Lauryl Maltose Neopentyl Glycol

• Macromolecule: Name: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 32 / Number of copies: 1 / Formula: AV0
• Molecular weight: Theoretical: 1.005188 KDa

Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

Macromolecule #33: [(1~{R},5~{S})-3,3,5-trimethyl-5-oxidanyl-4-[(3~{E},5~{E},7~{E},9...

• Macromolecule: Name: [(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; type: ligand / ID: 33 / Number of copies: 4 / Formula: A1L6D
• Molecular weight: Theoretical: 658.906 Da

Macromolecule #34: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

• Macromolecule: Name: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL; type: ligand / ID: 34 / Number of copies: 1 / Formula: SQD
• Molecular weight: Theoretical: 795.116 Da

Chemical component information

ChemComp-SQD:
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

Macromolecule #35: [(2~{R})-3-[(2~{S},3~{R},4~{R},5~{R},6~{R})-6-(hexadecanoyloxymet...

• Macromolecule: Name: [(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; type: ligand / ID: 35 / Number of copies: 1 / Formula: A1I05
• Molecular weight: Theoretical: 1.025567 KDa

Macromolecule #36: water

• Macromolecule: Name: water / type: ligand / ID: 36 / Number of copies: 1558 / Formula: HOH
• Molecular weight: Theoretical: 18.015 Da

Chemical component information

ChemComp-HOH:
WATER

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Concentration: 0.8 mg/mL
• Buffer: pH: 6.5 / Component - Concentration: 20.0 mM / Component - Formula: C₆H₁₃NO₄S / Component - Name: MES; Details: 20 mM MES pH 6.5, 0.15M NaCl and 0.01% Lauryl maltose neopentyl glycol
• Grid: Model: Quantifoil / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: OTHER; Details: 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
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Details: Blotting time 2.5 sec..
• Details: Protein sample in buffer solution of 20 mM MES pH 6.5, 0.15M NaCl and 0.01% Lauryl maltose neopentyl glycol

Electron microscopy

• Microscope: TFS KRIOS
• Temperature: Min: 79.0 K / Max: 81.0 K
• Specialist optics: Energy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
• Image recording: Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 2 / Number real images: 32897 / Average exposure time: 3.16 sec. / Average electron dose: 40.0 e/Ų; Details: Two dataset were collected and merged together during data processing.
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
• Sample stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Details: Motion correction and CTF estimation were performed on the raw data in cryoSPARC's Live session
• Particle selection: Number selected: 5807142 / Details: Blob picking was selected initially.
• CTF correction: Details: CTF estimation were performed on the raw data in cryoSPARC's Live session; Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
• Startup model: Type of model: INSILICO MODEL; In silico model: Ab initio reconstruction was used to create initial models for both datasets.; Details: Data for Ab initio reconstruction were obtained from the dataset after two rounds 2d classification.
• Final reconstruction: Applied symmetry - Point group: C₁ (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 1.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION; Details: The particles from both datasets were converted into star files using csparc2star from the PyEM suite for further processing in RELION v5.0.0b.; Number images used: 532822
• Initial angle assignment: Type: ANGULAR RECONSTITUTION
• Final angle assignment: Type: ANGULAR RECONSTITUTION
• Final 3D classification: Number classes: 5 ; Details: For Dataset 1, two rounds of heterogeneous refinement were performed using five classes. Dataset 2 underwent eight rounds of heterogeneous refinement using five classes.

Atomic model buiding 1

• Initial model: Chain - Source name: SwissModel / Chain - Initial model type: in silico model
• Refinement: Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 21.6 / Target criteria: CCC in ChimeraX

Output model

PDB-9hyu:
Cryo-EM structure of the Chromera velia PSI supercomplex at 1.84 Angstrom resolution