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- EMDB-51227: Cryo-EM structure of Arabidopsis thaliana PSI-LHCI- a603-NH mutant -

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Basic information

Entry
Database: EMDB / ID: EMD-51227
TitleCryo-EM structure of Arabidopsis thaliana PSI-LHCI- a603-NH mutant
Map dataSharpened map
Sample
  • Organelle or cellular component: Photosystem I supercomplex (PSI-LHCI), Lhca3/Lhca4 a603-NH mutant
    • Protein or peptide: x 17 types
  • Ligand: x 11 types
KeywordsPSI-LHCI / Arabidopsis thaliana / light harvesting / far-red absorption / PHOTOSYNTHESIS
Function / homology
Function and homology information


photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / chloroplast stromal thylakoid / response to low light intensity stimulus / plastoglobule / response to high light intensity / chloroplast membrane / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I ...photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / chloroplast stromal thylakoid / response to low light intensity stimulus / plastoglobule / response to high light intensity / chloroplast membrane / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / thylakoid / chloroplast envelope / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plastid / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / response to cold / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / protein stabilization / protein domain specific binding / mRNA binding / magnesium ion binding / mitochondrion / extracellular region / metal ion binding / nucleus / cytosol
Similarity search - Function
Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / 4Fe-4S dicluster domain / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic ...Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / 4Fe-4S dicluster domain / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / 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 / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / 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 PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA / 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 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
Similarity search - Domain/homology
Photosystem I reaction center subunit IX / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Chlorophyll a-b binding protein 4, chloroplastic / Photosystem I reaction center subunit N, chloroplastic / Photosystem I reaction center subunit VIII / Photosystem I iron-sulfur center / Chlorophyll a-b binding protein 6, chloroplastic / Photosystem I reaction center subunit IV B, chloroplastic / Photosystem I reaction center subunit V, chloroplastic ...Photosystem I reaction center subunit IX / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Chlorophyll a-b binding protein 4, chloroplastic / Photosystem I reaction center subunit N, chloroplastic / Photosystem I reaction center subunit VIII / Photosystem I iron-sulfur center / Chlorophyll a-b binding protein 6, chloroplastic / Photosystem I reaction center subunit IV B, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit II-2, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit XI, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Photosystem I reaction center subunit VI-1, chloroplastic / Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic / Photosystem I chlorophyll a/b-binding protein 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsCapaldi S / Chaves-Sanjuan A / Bonnet DMV / Bassi R
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)101053983-GrInSunEuropean Union
CitationJournal: New Phytol / Year: 2025
Title: Structural determinants for red-shifted absorption in higher-plants Photosystem I.
Authors: Stefano Capaldi / Zeno Guardini / Daniele Montepietra / Vittorio Flavio Pagliuca / Antonello Amelii / Elena Betti / Chris John / Laura Pedraza-González / Lorenzo Cupellini / Benedetta ...Authors: Stefano Capaldi / Zeno Guardini / Daniele Montepietra / Vittorio Flavio Pagliuca / Antonello Amelii / Elena Betti / Chris John / Laura Pedraza-González / Lorenzo Cupellini / Benedetta Mennucci / Diane Marie Valerie Bonnet / Antonio Chaves-Sanjuan / Luca Dall'Osto / Roberto Bassi /
Abstract: Higher plants Photosystem I absorbs far-red light, enriched under vegetation canopies, through long-wavelength Chls to enhance photon capture. Far-red absorption originates from Chl pairs within the ...Higher plants Photosystem I absorbs far-red light, enriched under vegetation canopies, through long-wavelength Chls to enhance photon capture. Far-red absorption originates from Chl pairs within the Lhca3 and Lhca4 subunits of the LHCI antenna, known as the 'red cluster', including Chls a603 and a609. We used reverse genetics to produce an Arabidopsis mutant devoid of red-shifted absorption, and we obtained high-resolution cryogenic electron microscopy structures of PSI-LHCI complexes from both wild-type and mutant plants. Computed excitonic coupling values suggested contributions from additional nearby pigment molecules, namely Chl a615 and violaxanthin in the L2 site, to far-red absorption. We investigated the structural determinants of far-red absorption by producing further Arabidopsis transgenic lines and analyzed the spectroscopic effects of mutations targeting these chromophores. The two structures solved were used for quantum mechanics calculations, revealing that excitonic interactions alone cannot explain far-red absorption, while charge transfer states were needed for accurate spectral simulations. Our findings demonstrate that the molecular mechanisms of light-harvesting under shaded conditions rely on very precise tuning of chromophore interactions, whose understanding is crucial for designing light-harvesting complexes with engineered absorption spectra.
History
DepositionAug 1, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51227.png

Downloads & links

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Map

FileDownload / File: emd_51227.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 448 pix.
= 398.272 Å		0.89 Å/pix.
x 448 pix.
= 398.272 Å		0.89 Å/pix.
x 448 pix.
= 398.272 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.889 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-1.5575435 - 3.6113374
Average (Standard dev.)0.0021235617 (±0.075007096)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 398.272 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51227_msk_1.map
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Additional map: Unharpened map

Fileemd_51227_additional_1.map
AnnotationUnharpened map
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Half map: Half map A

Fileemd_51227_half_map_1.map
AnnotationHalf_map A
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Half map: Half map B

Fileemd_51227_half_map_2.map
AnnotationHalf_map B
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Sample components

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Entire : Photosystem I supercomplex (PSI-LHCI), Lhca3/Lhca4 a603-NH mutant

EntireName: Photosystem I supercomplex (PSI-LHCI), Lhca3/Lhca4 a603-NH mutant
Components
  • Organelle or cellular component: Photosystem I supercomplex (PSI-LHCI), Lhca3/Lhca4 a603-NH mutant
    • Protein or peptide: Chlorophyll a-b binding protein 6, chloroplastic
    • Protein or peptide: Photosystem I chlorophyll a/b-binding protein 2, chloroplastic
    • Protein or peptide: Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein 4, chloroplastic
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A1
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A2
    • Protein or peptide: Photosystem I iron-sulfur center
    • Protein or peptide: Photosystem I reaction center subunit II-2, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit IV B, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit III, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit V, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit VI-1, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit VIII
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: Photosystem I reaction center subunit XI, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit psaK, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit N, chloroplastic
  • Ligand: CHLOROPHYLL B
  • Ligand: CHLOROPHYLL A
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • 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-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: PHYLLOQUINONE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Supramolecule #1: Photosystem I supercomplex (PSI-LHCI), Lhca3/Lhca4 a603-NH mutant

SupramoleculeName: Photosystem I supercomplex (PSI-LHCI), Lhca3/Lhca4 a603-NH mutant
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Chlorophyll a-b binding protein 6, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein 6, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 22.522793 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString: AGNVGRIRMA AHWMPGEPRP AYLDGSAPGD FGFDPLGLGE VPANLERYKE SELIHCRWAM LAVPGILVPE ALGYGNWVKA QEWAALPGG QATYLGNPVP WGTLPTILAI EFLAIAFVEH QRSMEKDPEK KKYPGGAFDP LGYSKDPKKL EELKVKEIKN G RLALLAFV ...String:
AGNVGRIRMA AHWMPGEPRP AYLDGSAPGD FGFDPLGLGE VPANLERYKE SELIHCRWAM LAVPGILVPE ALGYGNWVKA QEWAALPGG QATYLGNPVP WGTLPTILAI EFLAIAFVEH QRSMEKDPEK KKYPGGAFDP LGYSKDPKKL EELKVKEIKN G RLALLAFV GFCVQQSAYP GTGPLENLAT HLADPWHNNI GDIVIPFN

UniProtKB: Chlorophyll a-b binding protein 6, chloroplastic

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Macromolecule #2: Photosystem I chlorophyll a/b-binding protein 2, chloroplastic

MacromoleculeName: Photosystem I chlorophyll a/b-binding protein 2, chloroplastic
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 23.448623 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString: RAVAADPDRP IWFPGSTPPE WLDGSLPGDF GFDPLGLSSD PDSLKWNVQA EIVHCRWAML GAAGIFIPEF LTKIGILNTP SWYTAGEQE YFTDKTTLFV VELILIGWAE GRRWADIIKP GSVNTDPVFP NNKLTGTDVG YPGGLWFDPL GWGSGSPAKL K ELRTKEIK ...String:
RAVAADPDRP IWFPGSTPPE WLDGSLPGDF GFDPLGLSSD PDSLKWNVQA EIVHCRWAML GAAGIFIPEF LTKIGILNTP SWYTAGEQE YFTDKTTLFV VELILIGWAE GRRWADIIKP GSVNTDPVFP NNKLTGTDVG YPGGLWFDPL GWGSGSPAKL K ELRTKEIK NGRLAMLAVM GAWFQHIYTG TGPIDNLFAH LADPGHATIF AAFTPK

UniProtKB: Photosystem I chlorophyll a/b-binding protein 2, chloroplastic

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Macromolecule #3: Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic

MacromoleculeName: Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 25.258818 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString: KAAATPPVKQ GANRPLWFAS SQSLSYLDGS LPGDYGFDPL GLSDPEGTGG FIEPRWLAYG EIIHGRFAML GAAGAIAPEI LGKAGLIPA ETALPWFQTG VIPPAGTYTY WADNYTLFVL EMALMGFAEH RRLQDWYNPG SMGKQYFLGL EKGLAGSGNP A YPGGPFFN ...String:
KAAATPPVKQ GANRPLWFAS SQSLSYLDGS LPGDYGFDPL GLSDPEGTGG FIEPRWLAYG EIIHGRFAML GAAGAIAPEI LGKAGLIPA ETALPWFQTG VIPPAGTYTY WADNYTLFVL EMALMGFAEH RRLQDWYNPG SMGKQYFLGL EKGLAGSGNP A YPGGPFFN PLGFGKDEKS LKELKLKEVK NGRLAMLAIL GYFIQGLVTG VGPYQNLLDH LADPVNNNVL TSLKFH

UniProtKB: Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic

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Macromolecule #4: Chlorophyll a-b binding protein 4, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein 4, chloroplastic / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 22.298283 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString: KKGEWLPGLA SPDYLTGSLA GDNGFDPLGL AEDPENLKWF VQAELVHGRW AMLGVAGMLL PEVFTKIGII NVPEWYDAGK EQYFASSST LFVIEFILFH YVEIRRWQDI KNPGSVNQDP IFKQYSLPKG EVGYPGGIFN PLNFAPTQEA KEKELANGRL A MLAFLGFV ...String:
KKGEWLPGLA SPDYLTGSLA GDNGFDPLGL AEDPENLKWF VQAELVHGRW AMLGVAGMLL PEVFTKIGII NVPEWYDAGK EQYFASSST LFVIEFILFH YVEIRRWQDI KNPGSVNQDP IFKQYSLPKG EVGYPGGIFN PLNFAPTQEA KEKELANGRL A MLAFLGFV VQHNVTGKGP FENLLQHLSD PWHNTIVQTF N

UniProtKB: Chlorophyll a-b binding protein 4, chloroplastic

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Macromolecule #5: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 83.180156 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString: MIIRSPEPEV KILVDRDPIK TSFEEWAKPG HFSRTIAKGP DTTTWIWNLH ADAHDFDSHT SDLEEISRKV FSAHFGQLSI IFLWLSGMY FHGARFSNYE AWLSDPTHIG PSAQVVWSIV GQEILNGDVG GGFRGIQITS GFFQIWRASG ITSELQLYCT A IGGLVFAA ...String:
MIIRSPEPEV KILVDRDPIK TSFEEWAKPG HFSRTIAKGP DTTTWIWNLH ADAHDFDSHT SDLEEISRKV FSAHFGQLSI IFLWLSGMY FHGARFSNYE AWLSDPTHIG PSAQVVWSIV GQEILNGDVG GGFRGIQITS GFFQIWRASG ITSELQLYCT A IGGLVFAA LMLFAGWFHY HKAAPKLAWF QDVESMLNHH LAGLLGLGSL SWAGHQVHVS LPINQFLNAG VDPKEIPLPH EF ILNRDLL AQLYPSFAEG ATPFFTLNWS KYAEFLTFRG GLDPVTGGLW LTDIAHHHLA IAILFLIAGH MYRTNWGIGH GIK DILEAH KGPFTGQGHK GLYEILTTSW HAQLSINLAM LGSLTIVVAH HMYSMPPYPY LATDYGTQLS LFTHHMWIGG FLIV GAAAH AAIFMVRDYD PTTRYNDLLD RVLRHRDAII SHLNWVCIFL GFHSFGLYIH NDTMSALGRP QDMFSDTAIQ LQPVF AQWI QNTHALAPGT TAPGATTSTS LTWGGGDLVA VGGKVALLPI PLGTADFLVH HIHAFTIHVT VLILLKGVLF ARSSRL IPD KANLGFRFPC DGPGRGGTCQ VSAWDHVFLG LFWMYNAISV VIFHFSWKMQ SDVWGSISDQ GVVTHITGGN FAQSSIT IN GWLRDFLWAQ ASQVIQSYGS SLSAYGLFFL GAHFVWAFSL MFLFSGRGYW QELIESIVWA HNKLKVAPAT QPRALSIV Q GRAVGVTHYL LGGIATTWAF FLARIIAVG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A1

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Macromolecule #6: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 82.448695 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString: MALRFPRFSQ GLAQDPTTRR IWFGIATAHD FENHDDITEE RLYQNIFASH FGQLAIIFLW TSGNLFHVAW QGNFEAWVQD PLHVRPIAH AIWDPHFGQP AVEAFTRGGA LGPVNIAYSG VYQWWYTIGL RTNGDLYTGA LFLLFLSAIS LIAGWLHLQP K WKPSVSWF ...String:
MALRFPRFSQ GLAQDPTTRR IWFGIATAHD FENHDDITEE RLYQNIFASH FGQLAIIFLW TSGNLFHVAW QGNFEAWVQD PLHVRPIAH AIWDPHFGQP AVEAFTRGGA LGPVNIAYSG VYQWWYTIGL RTNGDLYTGA LFLLFLSAIS LIAGWLHLQP K WKPSVSWF KNAESRLNHH LSGLFGVSSL AWTGHLVHVA IPGSRGEYVR WNNFLGVLPH PQGLGPLFTG QWNLYAQNPD SS SHLFGTS QGTGTAILTL LGGFHPQTQS LWLTDIAHHH LAIAILFLVA GHMYRTNFGI GHSIKDLLEA HIPPGGRLGR GHR GLYDTI NNSIHFQLGL ALASLGVITS LVAQHMYSLP AYAFIAQDFT TQAALYTHHQ YIAGFIMTGA FAHGAIFFIR DYNP EQNED NVLARMLDHK EAIISHLSWA SLFLGFHTLG LYVHNDVMLA FGTPEKQILI EPIFAQWIQS AHGKTSYGFD VLLSS TNSP AFNAGRSIWL PGWLNAINEN SNSLFLTIGP GDFLVHHAIA LGLHTTTLIL VKGALDARGS KLMPDKKDFG YSFPCD GPG RGGTCDISAW DAFYLAVFWM LNTIGWVTFY WHWKHITLWQ GNVSQFNESS TYLMGWLRDY LWLNSSQLIN GYNPFGM NS LSVWAWMFLF GHLVWATGFM FLISWRGYWQ ELIETLAWAH ERTPLANLIR WRDKPVALSI VQARLVGLAH FSVGYIFT Y AAFLIASTSG KFG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A2

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Macromolecule #7: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 9.049509 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString:
MSHSVKIYDT CIGCTQCVRA CPTDVLEMIP WDGCKAKQIA SAPRTEDCVG CKRCESACPT DFLSVRVYLW HETTRSMGLA Y

UniProtKB: Photosystem I iron-sulfur center

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Macromolecule #8: Photosystem I reaction center subunit II-2, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit II-2, chloroplastic
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 17.68417 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString:
EKTESSSAAP AVKEAPVGFT PPQLDPNTPS PIFAGSTGGL LRKAQVEEFY VITWNSPKEQ IFEMPTGGAA IMREGPNLLK LARKEQCLA LGTRLRSKYK ITYQFYRVFP NGEVQYLHPK DGVYPEKANP GREGVGLNMR SIGKNVSPIE VKFTGKQSYD L

UniProtKB: Photosystem I reaction center subunit II-2, chloroplastic

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Macromolecule #9: Photosystem I reaction center subunit IV B, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit IV B, chloroplastic
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 10.561903 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString:
AAEDTPPATA SSDSSSTTAA AAPAKVPAAK AKPPPIGPKR GSKVKILRKE SYWYKNVGSV VAVDQDPKTR YPVVVRFAKV NYANISTNN YALDEVEEVK

UniProtKB: Photosystem I reaction center subunit IV B, chloroplastic

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Macromolecule #10: Photosystem I reaction center subunit III, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit III, chloroplastic
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 17.31916 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString:
DISGLTPCKD SKQFAKREKQ QIKKLESSLK LYAPESAPAL ALNAQIEKTK RRFDNYGKYG LLCGSDGLPH LIVNGDQRHW GEFITPGIL FLYIAGWIGW VGRSYLIAIS GEKKPAMKEI IIDVPLASRI IFRGFIWPVA AYREFLNGDL IAKDV

UniProtKB: Photosystem I reaction center subunit III, chloroplastic

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Macromolecule #11: Photosystem I reaction center subunit V, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit V, chloroplastic
type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 11.000299 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString:
ELSPSIVISL STGLSLFLGR FVFFNFQREN VAKQGLPEQN GKTHFEAGDD RAKEYVSLLK SNDPIGFNIV DVLAWGSIGH IVAYYILAT SSNGYDPSFF G

UniProtKB: Photosystem I reaction center subunit V, chloroplastic

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Macromolecule #12: Photosystem I reaction center subunit VI-1, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit VI-1, chloroplastic
type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 10.366769 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString:
KYGDKSVYFD LEDLGNTTGQ WDVYGSDAPS PYNPLQSKFF ETFAAPFTKR GLLLKFLILG GGSLLTYVSA TSTGEVLPIK RGPQEPPKL GPRGKL

UniProtKB: Photosystem I reaction center subunit VI-1, chloroplastic

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Macromolecule #13: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 4.137024 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString:
MTTFNNLPSI FVPLVGLVFP AIAMASLFLH IQKNKIF

UniProtKB: Photosystem I reaction center subunit VIII

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Macromolecule #14: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 5.021978 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString:
MRDLKTYLSV APVISTLWFA ALAGLLIEIN RLFPDALIFP FFSF

UniProtKB: Photosystem I reaction center subunit IX

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Macromolecule #15: Photosystem I reaction center subunit XI, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit XI, chloroplastic
type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 17.982693 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString:
AVKSDKTTFQ VVQPINGDPF IGSLETPVTS SPLIAWYLSN LPGYRTAVNP LLRGVEVGLA HGFFLVGPFV KAGPLRNTAY AGSAGSLAA AGLVVILSMC LTIYGISSFK EGEPSIAPSL TLTGRKKQPD QLQTADGWAK FTGGFFFGGI SGVTWAYFLL Y VLDLPYFV K

UniProtKB: Photosystem I reaction center subunit XI, chloroplastic

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Macromolecule #16: Photosystem I reaction center subunit psaK, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit psaK, chloroplastic
type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 8.46877 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString:
DFIGSSTNLI MVTSTTLMLF AGRFGLAPSA NRKATAGLRL EARDSGLQTG DPAGFTLADT LACGTVGHII GVGVVLGLKN IGAI

UniProtKB: Photosystem I reaction center subunit psaK, chloroplastic

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Macromolecule #17: Photosystem I reaction center subunit N, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit N, chloroplastic
type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 9.720043 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString:
GVIDEYLERS KTNKELNDKK RLATSGANFA RAFTVQFGSC KFPENFTGCQ DLAKQKKVPF ISEDIALECE GKDKYKCGSN VFWKW

UniProtKB: Photosystem I reaction center subunit N, chloroplastic

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Macromolecule #18: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 18 / Number of copies: 12 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

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Macromolecule #19: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 19 / Number of copies: 142 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #20: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

MacromoleculeName: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 20 / Number of copies: 5 / Formula: LUT
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-LUT:
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

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Macromolecule #21: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...

MacromoleculeName: (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: 21 / Number of copies: 4 / Formula: XAT
Molecular weightTheoretical: 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

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Macromolecule #22: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 22 / Number of copies: 5 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM

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Macromolecule #23: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 23 / Number of copies: 2 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #24: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 24 / Number of copies: 27 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #25: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 25 / Number of copies: 3 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #26: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 26 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #27: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 27 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #28: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 28 / Number of copies: 1 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationName
10.0 mMHEPES
0.05 %n-Dodecyl-Beta-Maltoside
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 115589
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 36596
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9gbi


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9gc2:
Cryo-EM structure of Arabidopsis thaliana PSI-LHCI- a603-NH mutant

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