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- EMDB-36021: Cryo-EM structure of the Arabidopsis thaliana photosystem I(PSI-L... -

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Basic information

Entry
Database: EMDB / ID: EMD-36021
TitleCryo-EM structure of the Arabidopsis thaliana photosystem I(PSI-LHCII-ST2)
Map data
Sample
  • Complex: photosystem I
    • Protein or peptide: x 19 types
  • Ligand: x 12 types
Keywordsphotosystem I / PSI / CELL CYCLE / PHOTOSYNTHESIS
Function / homology
Function and homology information


response to desiccation / photosynthesis, light harvesting in photosystem II / cellular response to abscisic acid stimulus / PSII associated light-harvesting complex II / cellular response to water deprivation / response to red light / photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / response to low light intensity stimulus ...response to desiccation / photosynthesis, light harvesting in photosystem II / cellular response to abscisic acid stimulus / PSII associated light-harvesting complex II / cellular response to water deprivation / response to red light / photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / response to low light intensity stimulus / chloroplast stromal thylakoid / plastoglobule / regulation of stomatal closure / response to high light intensity / chloroplast membrane / response to far red light / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / thylakoid / apoplast / photosynthesis, light harvesting / response to fructose / chloroplast envelope / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosynthetic electron transport chain / photosystem I / photosystem II / plastid / chlorophyll binding / chloroplast thylakoid membrane / positive regulation of reactive oxygen species biosynthetic process / response to light stimulus / 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 / plasma membrane / cytosol
Similarity search - Function
Photosystem I PsaO / PsaO transmembrane domain / 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 PsaO / PsaO transmembrane domain / 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 / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / 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
Chlorophyll a-b binding protein 2, chloroplastic / Chlorophyll a-b binding protein 4, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Chlorophyll a-b binding protein 6, chloroplastic / Photosystem I subunit O / Photosystem I reaction center subunit V, chloroplastic ...Chlorophyll a-b binding protein 2, chloroplastic / Chlorophyll a-b binding protein 4, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Chlorophyll a-b binding protein 6, chloroplastic / Photosystem I subunit O / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit IV A, chloroplastic / Photosystem I reaction center subunit II-2, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Chlorophyll a-b binding protein 2.1, chloroplastic / Photosystem I reaction center subunit XI, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Photosystem I reaction center subunit VI-2, 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: 2.79 Å
AuthorsChen SJB / Wu JH / Sui SF / Zhang LX
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Mol Plant / Year: 2023
Title: Regulatory dynamics of the higher-plant PSI-LHCI supercomplex during state transitions.
Authors: Jianghao Wu / Shuaijiabin Chen / Chao Wang / Weijun Lin / Chao Huang / Chengxu Fan / Dexian Han / Dandan Lu / Xiumei Xu / SenFang Sui / Lixin Zhang /
Abstract: State transition is a fundamental light acclimation mechanism of photosynthetic organisms in response to the environmental light conditions. This process rebalances the excitation energy between ...State transition is a fundamental light acclimation mechanism of photosynthetic organisms in response to the environmental light conditions. This process rebalances the excitation energy between photosystem I (PSI) and photosystem II through regulated reversible binding of the light-harvesting complex II (LHCII) to PSI. However, the structural reorganization of PSI-LHCI, the dynamic binding of LHCII, and the regulatory mechanisms underlying state transitions are less understood in higher plants. In this study, using cryoelectron microscopy we resolved the structures of PSI-LHCI in both state 1 (PSI-LHCI-ST1) and state 2 (PSI-LHCI-LHCII-ST2) from Arabidopsis thaliana. Combined genetic and functional analyses revealed novel contacts between Lhcb1 and PsaK that further enhanced the binding of the LHCII trimer to the PSI core with the known interactions between phosphorylated Lhcb2 and the PsaL/PsaH/PsaO subunits. Specifically, PsaO was absent in the PSI-LHCI-ST1 supercomplex but present in the PSI-LHCI-LHCII-ST2 supercomplex, in which the PsaL/PsaK/PsaA subunits undergo several conformational changes to strengthen the binding of PsaO in ST2. Furthermore, the PSI-LHCI module adopts a more compact configuration with shorter Mg-to-Mg distances between the chlorophylls, which may enhance the energy transfer efficiency from the peripheral antenna to the PSI core in ST2. Collectively, our work provides novel structural and functional insights into the mechanisms of light acclimation during state transitions in higher plants.
History
DepositionApr 26, 2023-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36021.png

Downloads & links

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Map

FileDownload / File: emd_36021.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.09 Å/pix.
x 336 pix.
= 365.232 Å		1.09 Å/pix.
x 336 pix.
= 365.232 Å		1.09 Å/pix.
x 336 pix.
= 365.232 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.59
Minimum - Maximum-20.964054000000001 - 38.962440000000001
Average (Standard dev.)0.021764295 (±1.1566241)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 365.232 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : photosystem I

EntireName: photosystem I
Components
  • Complex: photosystem I
    • 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 A, 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-2, 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 psaK, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit XI, chloroplastic
    • Protein or peptide: Photosystem I subunit O
    • Protein or peptide: Chlorophyll a-b binding protein 2, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein 2.1, chloroplastic
  • Ligand: CHLOROPHYLL B
  • Ligand: CHLOROPHYLL A
  • 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: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: PHYLLOQUINONE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL

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Supramolecule #1: photosystem I

SupramoleculeName: photosystem I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#19
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: 26.021895 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString: MASNSLMSCG IAAVYPSLLS SSKSKFVSAG VPLPNAGNVG RIRMAAHWMP GEPRPAYLDG SAPGDFGFDP LGLGEVPANL ERYKESELI HCRWAMLAVP GILVPEALGY GNWVKAQEWA ALPGGQATYL GNPVPWGTLP TILAIEFLAI AFVEHQRSME K DPEKKKYP ...String:
MASNSLMSCG IAAVYPSLLS SSKSKFVSAG VPLPNAGNVG RIRMAAHWMP GEPRPAYLDG SAPGDFGFDP LGLGEVPANL ERYKESELI HCRWAMLAVP GILVPEALGY GNWVKAQEWA ALPGGQATYL GNPVPWGTLP TILAIEFLAI AFVEHQRSME K DPEKKKYP GGAFDPLGYS KDPKKLEELK VKEIKNGRLA LLAFVGFCVQ QSAYPGTGPL ENLATHLADP WHNNIGDIVI PF N

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: 27.782814 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString: MASSLCASSA IAAISSPSFL GGKKLRLKKK LTVPAVSRPD ASVRAVAADP DRPIWFPGST PPEWLDGSLP GDFGFDPLGL SSDPDSLKW NVQAEIVHCR WAMLGAAGIF IPEFLTKIGI LNTPSWYTAG EQEYFTDKTT LFVVELILIG WAEGRRWADI I KPGSVNTD ...String:
MASSLCASSA IAAISSPSFL GGKKLRLKKK LTVPAVSRPD ASVRAVAADP DRPIWFPGST PPEWLDGSLP GDFGFDPLGL SSDPDSLKW NVQAEIVHCR WAMLGAAGIF IPEFLTKIGI LNTPSWYTAG EQEYFTDKTT LFVVELILIG WAEGRRWADI I KPGSVNTD PVFPNNKLTG TDVGYPGGLW FDPLGWGSGS PAKLKELRTK EIKNGRLAML AVMGAWFQHI YTGTGPIDNL FA HLADPGH ATIFAAFTPK

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: 29.206311 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString: MAAQALVSSS LTSSVQTARQ IFGSKPVASA SQKKSSFVVK AAATPPVKQG ANRPLWFASS QSLSYLDGSL PGDYGFDPLG LSDPEGTGG FIEPRWLAYG EIINGRFAML GAAGAIAPEI LGKAGLIPAE TALPWFQTGV IPPAGTYTYW ADNYTLFVLE M ALMGFAEH ...String:
MAAQALVSSS LTSSVQTARQ IFGSKPVASA SQKKSSFVVK AAATPPVKQG ANRPLWFASS QSLSYLDGSL PGDYGFDPLG LSDPEGTGG FIEPRWLAYG EIINGRFAML GAAGAIAPEI LGKAGLIPAE TALPWFQTGV IPPAGTYTYW ADNYTLFVLE M ALMGFAEH RRLQDWYNPG SMGKQYFLGL EKGLAGSGNP AYPGGPFFNP LGFGKDEKSL KELKLKEVKN GRLAMLAILG YF IQGLVTG 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: 27.760461 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString: MATVTTHASA SIFRPCTSKP RFLTGSSGRL NRDLSFTSIG SSAKTSSFKV EAKKGEWLPG LASPDYLTGS LAGDNGFDPL GLAEDPENL KWFVQAELVN GRWAMLGVAG MLLPEVFTKI GIINVPEWYD AGKEQYFASS STLFVIEFIL FHYVEIRRWQ D IKNPGSVN ...String:
MATVTTHASA SIFRPCTSKP RFLTGSSGRL NRDLSFTSIG SSAKTSSFKV EAKKGEWLPG LASPDYLTGS LAGDNGFDPL GLAEDPENL KWFVQAELVN GRWAMLGVAG MLLPEVFTKI GIINVPEWYD AGKEQYFASS STLFVIEFIL FHYVEIRRWQ D IKNPGSVN QDPIFKQYSL PKGEVGYPGG IFNPLNFAPT QEAKEKELAN GRLAMLAFLG FVVQHNVTGK GPFENLLQHL SD PWHNTIV QTFN

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: 83.315367 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString: MIIRSPEPEV KILVDRDPIK TSFEEWAKPG HFSRTIAKGP DTTTWIWNLH ADAHDFDSHT SDLEEISRKV FSAHFGQLSI IFLWLSGMY FHGARFSNYE AWLSDPTHIG PSAQVVWPIV GQEILNGDVG GGFRGIQITS GFFQIWRASG ITSELQLYCT A IGALVFAA ...String:
MIIRSPEPEV KILVDRDPIK TSFEEWAKPG HFSRTIAKGP DTTTWIWNLH ADAHDFDSHT SDLEEISRKV FSAHFGQLSI IFLWLSGMY FHGARFSNYE AWLSDPTHIG PSAQVVWPIV GQEILNGDVG GGFRGIQITS GFFQIWRASG ITSELQLYCT A IGALVFAA LMLFAGWFHY HKAAPKLAWF QDVESMLNHH LAGLLGLGSL SWAGHQVHVS LPINQFLNAG VDPKEIPLPH EF ILNRDLL AQLYPSFAEG ATPFFTLNWS KYSEFLTFRG GLDPVTGGLW LTDIAHHHLA IAILFLIAGH MYRTNWGIGH GIK DILEAH KGPFTGQGHK GLYEILTTSW HAQLSLNLAM LGSLTIIVAH HMYSMPPYPY LATDYATQLS LFTHHMWIGG FLIV GAAAH AAIFMVRDYD PTNRYNDLLD RVLRHRDAII SHLNWVCIFL GFHSFGLYIH NDTMSALGRP QDMFSDTAIQ LQPVF AQWI QNTHALAPGV TAPGETASTS LTWGGGELVA VGGKVALLPI PLGTADFLVH HIHAFTIHVT VLILLKGVLF ARSSRL IPD KANLGFRFPC DGPGRGGTCQ VSAWDHVFLG LFWMYNAISV VIFHFSWKMQ SDVWGSISDQ GVVTHITGGN FAQSSIT IN GWLRDFLWAQ ASQVIQSYGS SLSAYGLFFL GAHFVWAFSL MFLFSGRGYW QELIESIVWA HNKLKVAPAT QPRALSII 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: 82.555883 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString: MALRFPRFSQ GLAQDPTTRR IWFGIATAHD FESHDDITEE RLYQNIFASH FGQLAIIFLW TSGNLFHVAW QGNFETWVQD PLHVRPIAH AIWDPHFGQP AVEAFTRGGA LGPVNIAYSG VYQWWYTIGL RTNEDLYTGA LFLLFLSALS LIGGWLHLQP K WKPRVSWF ...String:
MALRFPRFSQ GLAQDPTTRR IWFGIATAHD FESHDDITEE RLYQNIFASH FGQLAIIFLW TSGNLFHVAW QGNFETWVQD PLHVRPIAH AIWDPHFGQP AVEAFTRGGA LGPVNIAYSG VYQWWYTIGL RTNEDLYTGA LFLLFLSALS LIGGWLHLQP K WKPRVSWF KNAESRLNHH LSGLFGVSSL AWTGHLVHVA IPASRGEYVR WNNFLNVLPH PQGLGPLFTG QWNLYAQNPD SS SHLFGTS QGSGTAILTL LGGFHPQTQS LWLTDMAHHH LAIAILFLIA GHMYRTNFGI GHSIKDLLEA HIPPGGRLGR GHK GLYDTI NNSIHFQLGL ALASLGVITS LVAQHMYSLP AYAFIAQDFT TQAALYTHHQ YIAGFIMTGA FAHGAIFFIR DYNP EQNED NVLARMLDHK EAIISHLSWA SLFLGFHTLG LYVHNDVMLA FGTPEKQILI EPIFAQWIQS AHGKTSYGFD VLLSS TSGP AFNAGRSIWL PGWLNAINEN SNSLFLTIGP GDFLVHHAIA LGLHTTTLIL VKGALDARGS KLMPDKKDFG YSFPCD GPG RGGTCDISAW DAFYLAVFWM LNTIGWVTFY WHWKHITLWQ GNVSQFNESS TYLMGWLRDY LWLNSSQLIN GYNPFGM NS LSVWAWMFLF GHLVWATGFM FLISWRGYWQ ELIETLAWAH ERTPLANLIR WKDKPVALSI 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: 22.336598 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString: MATQAAGIFS PAITTTTSAV KKLHLFSSSH RPKSLSFTKT AIRAEKTESS SAAPAVKEAP VGFTPPQLDP NTPSPIFAGS TGGLLRKAQ VEEFYVITWN SPKEQIFEMP TGGAAIMREG PNLLKLARKE QCLALGTRLR SKYKITYQFY RVFPNGEVQY L HPKDGVYP ...String:
MATQAAGIFS PAITTTTSAV KKLHLFSSSH RPKSLSFTKT AIRAEKTESS SAAPAVKEAP VGFTPPQLDP NTPSPIFAGS TGGLLRKAQ VEEFYVITWN SPKEQIFEMP TGGAAIMREG PNLLKLARKE QCLALGTRLR SKYKITYQFY RVFPNGEVQY L HPKDGVYP EKANPGREGV GLNMRSIGKN VSPIEVKFTG KQSYDL

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

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

MacromoleculeName: Photosystem I reaction center subunit IV A, chloroplastic
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 14.984955 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString:
MAMTTASTVF VLPANVTSVA GASSSRSSVS FLPMRNAGSR LVVRAAEDPA PASSSSKDSP AAAAAPDGAT ATKPKPPPIG PKRGSKVKI LRRESYWFKN VGSVVAVDQD PKTRYPVVVR FAKVNYANIS TNNYALDEVE EVAA

UniProtKB: Photosystem I reaction center subunit IV A, 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: 24.203125 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString: MSLTIPANLV LNPRSNKSLT QSVPKSSARF VCSDDKSSSS TPQSMKAFSA AVALSSILLS APMPAVADIS GLTPCKDSKQ FAKREKQQI KKLESSLKLY APESAPALAL NAQIEKTKRR FDNYGKYGLL CGSDGLPHLI VNGDQRHWGE FITPGILFLY I AGWIGWVG ...String:
MSLTIPANLV LNPRSNKSLT QSVPKSSARF VCSDDKSSSS TPQSMKAFSA AVALSSILLS APMPAVADIS GLTPCKDSKQ FAKREKQQI KKLESSLKLY APESAPALAL NAQIEKTKRR FDNYGKYGLL CGSDGLPHLI VNGDQRHWGE FITPGILFLY I AGWIGWVG RSYLIAISGE KKPAMKEIII DVPLASRIIF RGFIWPVAAY REFLNGDLIA KDV

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: 17.103271 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString:
MATSASALLS PTTFSTAISH KNPNSISFHG LRPLRLGGSS SALPKLSTTG RKSSSAVVRA ELSPSIVISL STGLSLFLGR FVFFNFQRE NVAKQGLPEQ NGKTHFEAGD DRAKEYVSLL KSNDPIGFNI VDVLAWGSIG HIVAYYILAT SSNGYDPSFF G

UniProtKB: Photosystem I reaction center subunit V, chloroplastic

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Macromolecule #12: Photosystem I reaction center subunit VI-2, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit VI-2, chloroplastic
type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 15.291522 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString:
MASFATIAAV QPSAAVKGLG GSSLAGAKLF IKPSRQSFKT KSTRAGAVVA KYGDKSVYFD LEDLGNTTGQ WDVYGSDAPS PYNPLQSKF FETFAAPFTK RGLLLKFLIL GGGSLLTYVS ANSTGDVLPI KRGPQEPPKL GPRGKL

UniProtKB: Photosystem I reaction center subunit VI-2, 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: 5.011897 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString:
MRDLKTYLSV APVLSTLWFG SLAGLLIEIN RLFPDALTFP FFSF

UniProtKB: Photosystem I reaction center subunit IX

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

MacromoleculeName: Photosystem I reaction center subunit psaK, chloroplastic
type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 13.219431 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString:
MASTMMTTLP QFNGLRATKI SAAPVQGLAS VQPMRRKGNG ALGAKCDFIG SSTNLIMVTS TTLMLFAGRF GLAPSANRKA TAGLRLEAR DSGLQTGDPA GFTLADTLAC GTVGHIIGVG VVLGLKNIGA I

UniProtKB: Photosystem I reaction center subunit psaK, chloroplastic

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

MacromoleculeName: Photosystem I reaction center subunit XI, chloroplastic
type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 23.070557 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString: MAASASPMAS QLRSSFSSAS LSQRLAVPKG ISGAPFGVSP TKRVSSFTVR AVKSDKTTFQ VVQPINGDPF IGSLETPVTS SPLIAWYLS NLPGYRTAVN PLLRGVEVGL AHGFFLVGPF VKAGPLRNTA YAGSAGSLAA AGLVVILSMC LTIYGISSFK E GEPSIAPS ...String:
MAASASPMAS QLRSSFSSAS LSQRLAVPKG ISGAPFGVSP TKRVSSFTVR AVKSDKTTFQ VVQPINGDPF IGSLETPVTS SPLIAWYLS NLPGYRTAVN PLLRGVEVGL AHGFFLVGPF VKAGPLRNTA YAGSAGSLAA AGLVVILSMC LTIYGISSFK E GEPSIAPS LTLTGRKKQP DQLQTADGWA KFTGGFFFGG ISGVTWAYFL LYVLDLPYFV K

UniProtKB: Photosystem I reaction center subunit XI, chloroplastic

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Macromolecule #17: Photosystem I subunit O

MacromoleculeName: Photosystem I subunit O / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 15.15647 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString:
MAATFATPST VIGLGGSSIT TKPFSSSFLK PTLSAKNPLR LAGASGGRVT CFERNWLRRD LNVVGFGLIG WLAPSSIPAI NGKSLTGLF FDSIGTELAH FPTPPALTSQ FWLWLVTWHL GLFLCLTFGQ IGFKGRTEDY F

UniProtKB: Photosystem I subunit O

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Macromolecule #18: Chlorophyll a-b binding protein 2, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein 2, chloroplastic / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 28.250984 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString: MAASTMALSS PAFAGKAVNL SPAASEVLGS GRVTMRKTVA KPKGPSGSPW YGSDRVKYLG PFSGESPSYL TGEFPGDYGW DTAGLSADP ETFARNRELE VIHSRWAMLG ALGCVFPELL ARNGVKFGEA VWFKAGSQIF SDGGLDYLGN PSLVHAQSIL A IWATQVIL ...String:
MAASTMALSS PAFAGKAVNL SPAASEVLGS GRVTMRKTVA KPKGPSGSPW YGSDRVKYLG PFSGESPSYL TGEFPGDYGW DTAGLSADP ETFARNRELE VIHSRWAMLG ALGCVFPELL ARNGVKFGEA VWFKAGSQIF SDGGLDYLGN PSLVHAQSIL A IWATQVIL MGAVEGYRVA GNGPLGEAED LLYPGGSFDP LGLATDPEAF AELKVKELKN GRLAMFSMFG FFVQAIVTGK GP IENLADH LADPVNNNAW AFATNFVPGK

UniProtKB: Chlorophyll a-b binding protein 2, chloroplastic

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Macromolecule #19: Chlorophyll a-b binding protein 2.1, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein 2.1, chloroplastic / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 28.753369 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString: MATSAIQQSS FAGQTALKPS NELLRKVGVS GGGRVTMRR(TPO) VKSTPQSIWY GPDRPKYLGP FSENTPSYLT GEYPGD YGW DTAGLSADPE TFAKNRELEV IHSRWAMLGA LGCTFPEILS KNGVKFGEAV WFKAGSQIFS EGGLDYLGNP NLIHAQS IL AIWAVQVVLM ...String:
MATSAIQQSS FAGQTALKPS NELLRKVGVS GGGRVTMRR(TPO) VKSTPQSIWY GPDRPKYLGP FSENTPSYLT GEYPGD YGW DTAGLSADPE TFAKNRELEV IHSRWAMLGA LGCTFPEILS KNGVKFGEAV WFKAGSQIFS EGGLDYLGNP NLIHAQS IL AIWAVQVVLM GFIEGYRIGG GPLGEGLDPL YPGGAFDPLN LAEDPEAFSE LKVKELKNGR LAMFSMFGFF VQAIVTGK G PIENLFDHLA DPVANNAWSY ATNFVPGN

UniProtKB: Chlorophyll a-b binding protein 2.1, chloroplastic

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Macromolecule #20: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 20 / Number of copies: 30 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

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Macromolecule #21: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 21 / Number of copies: 168 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #22: (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: 22 / Number of copies: 6 / 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 #23: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 23 / Number of copies: 9 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #24: (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: 24 / Number of copies: 11 / 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 #25: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 25 / Number of copies: 27 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #26: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 26 / Number of copies: 2 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #27: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 27 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #28: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 28 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #29: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 29 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #30: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 30 / Number of copies: 1 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #31: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY...

MacromoleculeName: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
type: ligand / ID: 31 / Number of copies: 3 / Formula: NEX
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-NEX:
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 188490
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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