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- EMDB-37513: Cryo-EM structure of the red-shifted Fittonia albivenis PSI-LHCI -

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Basic information

Entry
Database: EMDB / ID: EMD-37513
TitleCryo-EM structure of the red-shifted Fittonia albivenis PSI-LHCI
Map data
Sample
  • Complex: Photosystem I complex
    • Protein or peptide: x 18 types
  • Ligand: x 12 types
KeywordsComplex / PHOTOSYNTHESIS
Function / homology
Function and homology information


plastoglobule / chloroplast thylakoid / thylakoid / chloroplast envelope / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane ...plastoglobule / chloroplast thylakoid / thylakoid / chloroplast envelope / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / protein domain specific binding / mRNA binding / magnesium ion binding / metal ion binding / nucleus
Similarity search - Function
4Fe-4S dicluster domain / 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 PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ ...4Fe-4S dicluster domain / 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 PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / 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 / 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 P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit VIII / Photosystem I iron-sulfur center / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit III, chloroplastic
Similarity search - Component
Biological speciesFittonia albivenis (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsHuang GQ / Li XX / Sui SF / Qin XC
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Structure of the red-shifted Fittonia albivenis photosystem I.
Authors: Xiuxiu Li / Guoqiang Huang / Lixia Zhu / Chenyang Hao / Sen-Fang Sui / Xiaochun Qin /
Abstract: Photosystem I (PSI) from Fittonia albivenis, an Acanthaceae ornamental plant, is notable among green plants for its red-shifted emission spectrum. Here, we solved the structure of a PSI-light ...Photosystem I (PSI) from Fittonia albivenis, an Acanthaceae ornamental plant, is notable among green plants for its red-shifted emission spectrum. Here, we solved the structure of a PSI-light harvesting complex I (LHCI) supercomplex from F. albivenis at 2.46-Å resolution using cryo-electron microscopy. The supercomplex contains a core complex of 14 subunits and an LHCI belt with four antenna subunits (Lhca1-4) similar to previously reported angiosperm PSI-LHCI structures; however, Lhca3 differs in three regions surrounding a dimer of low-energy chlorophylls (Chls) termed red Chls, which absorb far-red beyond visible light. The unique amino acid sequences within these regions are exclusively shared by plants with strongly red-shifted fluorescence emission, suggesting candidate structural elements for regulating the energy state of red Chls. These results provide a structural basis for unraveling the mechanisms of light harvest and transfer in PSI-LHCI of under canopy plants and for designing Lhc to harness longer-wavelength light in the far-red spectral range.
History
DepositionSep 21, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37513.png

Downloads & links

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Map

FileDownload / File: emd_37513.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 324.75 Å		1.08 Å/pix.
x 300 pix.
= 324.75 Å		1.08 Å/pix.
x 300 pix.
= 324.75 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.047954 - 4.545464
Average (Standard dev.)0.0044723237 (±0.14624313)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.75 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37513_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37513_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Photosystem I complex

EntireName: Photosystem I complex
Components
  • Complex: Photosystem I complex
    • Protein or peptide: Chlorophyll a-b binding protein 1
    • Protein or peptide: Chlorophyll a-b binding protein 2
    • Protein or peptide: Chlorophyll a-b binding protein 3
    • Protein or peptide: Chlorophyll a-b binding protein 4
    • 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
    • Protein or peptide: Photosystem I reaction center subunit IV
    • Protein or peptide: Photosystem I reaction center subunit III, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit VIII
    • Protein or peptide: Photosystem I reaction center subunit VI
    • 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
    • Protein or peptide: Photosystem I reaction center subunit XI
    • Protein or peptide: Photosystem I reaction center subunit N
    • Protein or peptide: Photosystem I reaction center subunit O
  • 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: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: heptyl 1-thio-beta-D-glucopyranoside
  • Ligand: PHYLLOQUINONE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Supramolecule #1: Photosystem I complex

SupramoleculeName: Photosystem I complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18
Source (natural)Organism: Fittonia albivenis (plant)

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Macromolecule #1: Chlorophyll a-b binding protein 1

MacromoleculeName: Chlorophyll a-b binding protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Fittonia albivenis (plant)
Molecular weightTheoretical: 26.77368 KDa
SequenceString: MAANSMMTCG VAVAACPSVL SSSKSRFAAP VSLGYAATTS SRFSMSAEWF PGQPRPDHLD GSAPADFGFD PLGLGVEPEL LERYKESEV YHCRWAMLAV PGILVPEALG LGNWVKAQEW AAIPGGQATY LGNPVPWGTL PTILVIEFLA IAFVEHQRTL E KDIEKKKY ...String:
MAANSMMTCG VAVAACPSVL SSSKSRFAAP VSLGYAATTS SRFSMSAEWF PGQPRPDHLD GSAPADFGFD PLGLGVEPEL LERYKESEV YHCRWAMLAV PGILVPEALG LGNWVKAQEW AAIPGGQATY LGNPVPWGTL PTILVIEFLA IAFVEHQRTL E KDIEKKKY PGGAFDPLGF SKDPKKFEEY KVKEIKNGRL AMLAFVGFCV QQSARPGTGP VENLLSHLAD PWHNNIGDII IP RNISPY

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Macromolecule #2: Chlorophyll a-b binding protein 2

MacromoleculeName: Chlorophyll a-b binding protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Fittonia albivenis (plant)
Molecular weightTheoretical: 28.533506 KDa
SequenceString: MASACASSAI AAAFSSPSSQ RIGTTKASFF GGRKLRVAKF AAPVTARSVT TATFAPDPNR PLWFPGSTPP PWLDGSLPAD FGFDPLGLA SDPDSLKWNV QAEIVHCRWA MLGAAGIFIP ELLTKIGILN TPSWYSAGEL QYFTDTTTLF IVELFFIGWA E GRRWADIL ...String:
MASACASSAI AAAFSSPSSQ RIGTTKASFF GGRKLRVAKF AAPVTARSVT TATFAPDPNR PLWFPGSTPP PWLDGSLPAD FGFDPLGLA SDPDSLKWNV QAEIVHCRWA MLGAAGIFIP ELLTKIGILN TPSWYSAGEL QYFTDTTTLF IVELFFIGWA E GRRWADIL KPGCVNTDPI FPNNKLTGTD VGYPGGLWFD PLGWGTGSPE KLKELRTKEI KNGRLAMLAV MGAWFQHVYT GT GPIDNLS AHLADPGHAT VFAAFSPK

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Macromolecule #3: Chlorophyll a-b binding protein 3

MacromoleculeName: Chlorophyll a-b binding protein 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Fittonia albivenis (plant)
Molecular weightTheoretical: 29.766748 KDa
SequenceString: MAAQALVSSS SICSSADAVR QTLGRRPVRS SRKASFVVKA ESSPPVKQGA DRQLWFASKQ SLSYLNGSLP GDYGFDPLGL SDPEGAGFW FQPRWLSYGE VFNGRTAMVG VIGCLAPEIL GKAGLIPPET ALPWFKTGVF PPAGSYEYWA DPYTLFVFEL G LVGFAEHR ...String:
MAAQALVSSS SICSSADAVR QTLGRRPVRS SRKASFVVKA ESSPPVKQGA DRQLWFASKQ SLSYLNGSLP GDYGFDPLGL SDPEGAGFW FQPRWLSYGE VFNGRTAMVG VIGCLAPEIL GKAGLIPPET ALPWFKTGVF PPAGSYEYWA DPYTLFVFEL G LVGFAEHR RYQDWSNPGS MGKQYFLGLE KGLGGSGDPA YPGGPFFNPL GLGKDEKSMW DYKVKEVKNG RLAMLAMLGF FV QAPVTGV GPYQNLLDHL ADPFNNNIFT NFKFY

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Macromolecule #4: Chlorophyll a-b binding protein 4

MacromoleculeName: Chlorophyll a-b binding protein 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Fittonia albivenis (plant)
Molecular weightTheoretical: 27.51034 KDa
SequenceString: MAASVAAQSP VAVFRPRFLT GAPGKLNRPS VTVKQAVSSR GSFKVEAEKG EWLPGLPSPA YLDGSLPGDN GFDPLGLAED PENLKWYIQ AELVNSRWAM LGVAGMLLPE VFTYLGIINV PKWYDAGKSE YFASSSTLFV IEFILFHYVE IRRWQDIKNP G CVNQDPIF ...String:
MAASVAAQSP VAVFRPRFLT GAPGKLNRPS VTVKQAVSSR GSFKVEAEKG EWLPGLPSPA YLDGSLPGDN GFDPLGLAED PENLKWYIQ AELVNSRWAM LGVAGMLLPE VFTYLGIINV PKWYDAGKSE YFASSSTLFV IEFILFHYVE IRRWQDIKNP G CVNQDPIF KNYSLPPHEC GYPGSVFNPL NFEPTLEAKE KELANGRLAM LAFLGFIVQH NVTGKGPFDN LVQHVADPWH NT IINTIRG Y

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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
Details: Sequence reference for Fittonia albivenis is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A8A0WPY6.
Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Fittonia albivenis (plant)
Molecular weightTheoretical: 83.138141 KDa
SequenceString: MIIRSPEPEV KILVDKDPVK TSFEEWAKPG HFSRTIAKGP DTTTWIWNLH ADAHDFDSHT SDLEEISRKV FSAHFGQLSI IFLWLSGMY FHGARFSNYE AWLSDPTHIG PSAQVVWPIV GQEILNGDVG GGFRGIQITS GFFQMWRASG ITSELQLYCT A IGALIFAA ...String:
MIIRSPEPEV KILVDKDPVK TSFEEWAKPG HFSRTIAKGP DTTTWIWNLH ADAHDFDSHT SDLEEISRKV FSAHFGQLSI IFLWLSGMY FHGARFSNYE AWLSDPTHIG PSAQVVWPIV GQEILNGDVG GGFRGIQITS GFFQMWRASG ITSELQLYCT A IGALIFAA LMLFAGWFHY HKAAPKLAWF QDVESMLNHH LAGLLGLGSL GWAGHQVHVS LPINQFLNAG VDPKEIPLPH EF ILNRDLL SQLYPSFAEG ATPFFTLNWS KYAEFLTFRG GLDPVTGGLW LTDIAHHHLA IAILFLIAGH MYRTNWGIGH GLK DILEAH KGPFTGQGHK GLYEILTTSW HAQLSLNLAM LGSLTIVVAH HMYSMPPYPY LATDYGTQLS LFTHHMWIGG FLIV GAAAH AAIFMVRDYD PTTRYNDLLD RVLRHRDAII SHLNWACIFL GFHSFGLYIH NDTMSALGRP QDMFSDTAIQ LQPVF AQWI QNTHALAPGA TAPSATASTS LTWGGGDLVA VGGKVALLPI PLGTADFLVH HIHAFTIHVT VLILLKGVLF ARSSRL IPD KANLGFRFPC DGPGRGGTCQ VSAWDHVFLG LFWMYNSISV 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
Details: Sequence reference for Fittonia albivenis is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id G9IB61.
Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Fittonia albivenis (plant)
Molecular weightTheoretical: 82.472664 KDa
SequenceString: MALRFPRFSQ GLAQDPTTRR IWFGIATAHD FESHDDITEE RLYQNIFASH FGQLAIIFLW TSGNLFHVAW QGNFESWVQD PLHVRPIAH AIWDPHFGQP AVEAFTRGGA LGPVNIAYSG VYQWWYTIGL RTNEDLYTGA LFLLFLSAIS LIAGWLHLQP K WKPSVSWF ...String:
MALRFPRFSQ GLAQDPTTRR IWFGIATAHD FESHDDITEE RLYQNIFASH FGQLAIIFLW TSGNLFHVAW QGNFESWVQD PLHVRPIAH AIWDPHFGQP AVEAFTRGGA LGPVNIAYSG VYQWWYTIGL RTNEDLYTGA LFLLFLSAIS LIAGWLHLQP K WKPSVSWF KNAESRLNHH LSGLFGVSSL AWTGHLVHVA IPGSRGEYVR WNNFLDVLPH PQGLGPLFTG QWNLYAQNPD SS SHLFGTS QGAGTAILTL LGGFHPQTQS LWLTDIAHHH LAIAFIFLVA GHMYRTNFGI GHSIKDLLDA HIPPGGRLGR GHK GLYDTI NNSLHFQLGL ALASLGVITS LVAQHMYSLP AYAFIAQDFT TQAALYTHHQ YIAGFIMTGA FAHGAIFFIR DYNP EQNED NVLARMLDHK EAIISHLSWA SLFLGFHTLG LYVHNDVMLA FGTPEKQILI EPIFAQWIQS AHGKTSYGFD VLLSS TSGP AFNAGRSIWL PGWLNAVNEN TNSLFLTIGP 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
Details: Sequence reference for Fittonia albivenis is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A4QJG7.
Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Fittonia albivenis (plant)
Molecular weightTheoretical: 9.049509 KDa
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

MacromoleculeName: Photosystem I reaction center subunit II / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Fittonia albivenis (plant)
Molecular weightTheoretical: 21.036172 KDa
SequenceString:
MASLFTLSSP WKQSLAPQFT AAKNPKPLPR AVAMPIRAMA PEESAPAGFT PPQLDPSTPS PIFGGSTGGL LRKAQEEEFY VITWESPKE QVFEMPTGGA AIMREGPNLL KLARKEQCLA LGTRLRSKYK INYQFYRVFP NGEVQYLHPK DGVYPEKVNE G RTGVGVNL RSIGKNVNPI EVKFTGKQVY DL

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Macromolecule #9: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Fittonia albivenis (plant)
Molecular weightTheoretical: 16.28236 KDa
SequenceString:
MATTGMASAA CTFAVAPNFA SSTATPKPAM VFFSTKPRRN LRLFMVRAGD DEPEAPAPPP EPEVESDTPA AATATTTAEP KVAKTPSVG PPRGSKVRIL RRESYWYKGV GSVVTVDQDP KTRYPVVVRF DKVNYANIST NNYALDEVEQ VA

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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
Details: Sequence reference for Fittonia albivenis is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id Q9SHE8.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Fittonia albivenis (plant)
Molecular weightTheoretical: 24.203125 KDa
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 VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Fittonia albivenis (plant)
Molecular weightTheoretical: 15.873991 KDa
SequenceString:
MASSFLSTPT FQGLRPLNKA TDSPRSLPLC RPVSVSATRK RNVAVKAELN PSLVISLSTG VSLFLGRFVF FNFQRENVGK QVPSQNGIS HFEAGDERAK EYVSLLKSND PVGFNIVDVL AWGSIGHIVA YYILATSSNG YDPNFF

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Macromolecule #12: Photosystem I reaction center subunit VI

MacromoleculeName: Photosystem I reaction center subunit VI / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Fittonia albivenis (plant)
Molecular weightTheoretical: 15.201321 KDa
SequenceString:
MASLATFAAA HPAAVKGLAG SSISGTKLHI RPSRRVGVKS SNYRAGAVVA KYGEKSVYFD LEDIANTTGQ WDVYGSDAPS PYNGLQSKF FETFAAPFTK RGLLLKFLLL GGGATLAFVS SQATGDDLPI VKGPQLPPQP GPRGKI

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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
Details: Sequence reference for Fittonia albivenis is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A8A9WIB9.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Fittonia albivenis (plant)
Molecular weightTheoretical: 3.930826 KDa
SequenceString:
MTAFNLPSIF VPLVGLVFPA IAMASLFLHV QKNKIV

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
Details: Sequence reference for Fittonia albivenis is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id Q3C1K9.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Fittonia albivenis (plant)
Molecular weightTheoretical: 5.029914 KDa
SequenceString:
MRDLKTYLSV APVLSTLWFG ALAGLLIEIN RFFPDALTFP FFSF

UniProtKB: Photosystem I reaction center subunit IX

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Macromolecule #15: Photosystem I reaction center subunit psaK

MacromoleculeName: Photosystem I reaction center subunit psaK / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Fittonia albivenis (plant)
Molecular weightTheoretical: 13.435645 KDa
SequenceString:
MAAAVTTSLP QFNGLKPQLS ASSISPSKSL VAVRPLRRRG QGALGARCDY FGSPTNLIMV TSTTLLLFAG RFGLAPSANR KATAGLKLE VRDAGLQTGD PAGFTLADTL ACGAVGHIIG VGVVLGLKSI SVI

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Macromolecule #16: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Fittonia albivenis (plant)
Molecular weightTheoretical: 23.094725 KDa
SequenceString: MATSTMASLG QQQLASSLCP SFSRLPTPKG ISAAPFTFSR RRTSIIKASV VPEKPTYQVI QPINGDPFIG SLETPITSSP LIAWYLSNL PGYRTAVDPL LRGIEVGLAH GYLLVGPFVI TGPLRNAPNH GAVGSLGAAG LIVILSITLT MYGIASFKEG D PSTAPSLT ...String:
MATSTMASLG QQQLASSLCP SFSRLPTPKG ISAAPFTFSR RRTSIIKASV VPEKPTYQVI QPINGDPFIG SLETPITSSP LIAWYLSNL PGYRTAVDPL LRGIEVGLAH GYLLVGPFVI TGPLRNAPNH GAVGSLGAAG LIVILSITLT MYGIASFKEG D PSTAPSLT LTGRKKVPDP LQTADGWARF TGGFFFGGIS GVIWAYFLLY VLDLPYFVK

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Macromolecule #17: Photosystem I reaction center subunit N

MacromoleculeName: Photosystem I reaction center subunit N / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Fittonia albivenis (plant)
Molecular weightTheoretical: 18.673109 KDa
SequenceString:
MAAINSSSVL ACNYALSAAG TELSSKVVNS VASPVSVAHP PRLPVIRAQQ QQQPQSAAAG SRRAALFGLG AALLAVSTNA NANASVIDY YLEKSKANKE LNDKKRLATT DANFARAYTV EFGTCKFPEN FTGCQDLAKQ KKVPFLSEDL DIECEGKDIY K CGSNVFWK WNEIK

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Macromolecule #18: Photosystem I reaction center subunit O

MacromoleculeName: Photosystem I reaction center subunit O / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Fittonia albivenis (plant)
Molecular weightTheoretical: 15.404838 KDa
SequenceString:
MAASTMAAAS TVVGLGTSSL IAPKKLNLSS GFLKSPIQAR NPLRLAQASG GKFTCFERDW LRTDLNVIGF GLIGWLAPSS IPAINGNSL TGLFFSSIGP ELAHFPTGPA VTSPFWLWMV LWHLGLFLTL TFGQIGFKGR SEGYF

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Macromolecule #19: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 19 / Number of copies: 12 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

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Macromolecule #20: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 20 / Number of copies: 150 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #21: (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: 21 / Number of copies: 7 / 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 #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: 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 #23: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 23 / Number of copies: 26 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #24: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 24 / 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 #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: heptyl 1-thio-beta-D-glucopyranoside

MacromoleculeName: heptyl 1-thio-beta-D-glucopyranoside / type: ligand / ID: 26 / Number of copies: 10 / Formula: HTG
Molecular weightTheoretical: 294.408 Da
Chemical component information

ChemComp-HTG:
heptyl 1-thio-beta-D-glucopyranoside / detergent*YM

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Macromolecule #27: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 27 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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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: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 29 / 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 #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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 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: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 157342
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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