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- EMDB-63799: Cryo-EM structure of violaxanthin-chlorophyll-a-binding protein w... -

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Basic information

Entry
Database: EMDB / ID: EMD-63799
TitleCryo-EM structure of violaxanthin-chlorophyll-a-binding protein with red shifted Chl a (rVCP) from Trachydiscus minutus at 2.4 angstrom
Map data
Sample
  • Complex: Tetrameric light-harvesting complex from Trachydiscus minutus.
    • Protein or peptide: Light-harvesting complex
    • Protein or peptide: light-harvesting complex
  • Ligand: CHLOROPHYLL A
  • Ligand: [(2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E})-17-[(4~{S},6~{R})-4-acetyloxy-2,2,6-trimethyl-6-oxidanyl-cyclohexylidene]-6,11,15-trimethyl-2-[(~{E})-2-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]ethenyl]heptadeca-2,4,6,8,10,12,14,16-octaenyl] octanoate
  • 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: water
Keywordsviolaxanthin / vaucheriaxanthin / chlorophyll a / VCP / tetramer / red Chlorophyll / PHOTOSYNTHESIS
Biological speciesTrachydiscus minutus (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.42 Å
AuthorsSeki S / Litvin R / Bina D / Tanaka H / Miyata T / Namba K / Kurisu G / Polivka T / Fujii R
Funding support Japan, 5 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP23ama121003 Japan
Japan Society for the Promotion of Science (JSPS)K23KJ1834 Japan
Japan Science and TechnologyJPMJFS2138 Japan
Japan Science and TechnologyJPMJCR20E1 Japan
Japan Society for the Promotion of Science (JSPS)23H04958 Japan
CitationJournal: To Be Published
Title: Cryo-EM structure of violaxanthin-chlorophyll a protein with red Chl: rVCP from Trachydiscus minutus.
Authors: Seki S / Litvin R / Bina D / Miyata T / Tanaka H / Namba K / Kurisu G / Polivka T / Fujii R
History
DepositionMar 17, 2025-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63799.png

Downloads & links

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Map

FileDownload / File: emd_63799.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 256 pix.
= 223.488 Å		0.87 Å/pix.
x 256 pix.
= 223.488 Å		0.87 Å/pix.
x 256 pix.
= 223.488 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.873 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.573859 - 2.5377016
Average (Standard dev.)0.0017389175 (±0.067175284)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 223.488 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63799_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63799_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tetrameric light-harvesting complex from Trachydiscus minutus.

EntireName: Tetrameric light-harvesting complex from Trachydiscus minutus.
Components
  • Complex: Tetrameric light-harvesting complex from Trachydiscus minutus.
    • Protein or peptide: Light-harvesting complex
    • Protein or peptide: light-harvesting complex
  • Ligand: CHLOROPHYLL A
  • Ligand: [(2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E})-17-[(4~{S},6~{R})-4-acetyloxy-2,2,6-trimethyl-6-oxidanyl-cyclohexylidene]-6,11,15-trimethyl-2-[(~{E})-2-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]ethenyl]heptadeca-2,4,6,8,10,12,14,16-octaenyl] octanoate
  • 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: water

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Supramolecule #1: Tetrameric light-harvesting complex from Trachydiscus minutus.

SupramoleculeName: Tetrameric light-harvesting complex from Trachydiscus minutus.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Trachydiscus minutus (eukaryote)
Molecular weightTheoretical: 120 KDa

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Macromolecule #1: Light-harvesting complex

MacromoleculeName: Light-harvesting complex / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Trachydiscus minutus (eukaryote)
Molecular weightTheoretical: 24.611354 KDa
SequenceString: SDNTRTLPDR ENSCPGLLLL LLPIMKTAIA LLPFLGAATA FVTPMSKTSM ARGRSLQMSF DDEAGAIQWF PPSPGYWDPL GFVADGDTE KFSKYRAIEI KHGRVAMLGA LDYFIKTPSG WHLPGKLGDV DIDSIPVGLG AIKAVPPLGW VQILLFASAL E FLAPQKED ...String:
SDNTRTLPDR ENSCPGLLLL LLPIMKTAIA LLPFLGAATA FVTPMSKTSM ARGRSLQMSF DDEAGAIQWF PPSPGYWDPL GFVADGDTE KFSKYRAIEI KHGRVAMLGA LDYFIKTPSG WHLPGKLGDV DIDSIPVGLG AIKAVPPLGW VQILLFASAL E FLAPQKED QPPGAVQPAT PSFEQPGTLE YQTKEINNGR LAMIALAGLW LGELASGGTD PIVAFKTWVG I

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Macromolecule #2: light-harvesting complex

MacromoleculeName: light-harvesting complex / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Trachydiscus minutus (eukaryote)
Molecular weightTheoretical: 23.934508 KDa
SequenceString: MVAKSAALVV MGLSMASAFL APTPNNRASA QAPMKMAKSA ATKEFPFDDQ PGGVKWFPSS APYWDPLGFT NEKTEDEYWR IAHGEIKNG RLAMLAVTHY FVVGSGLRFP FKFGSVSTAD VPLGLGAIKA LPWAVWLQIA AFCLVLEVLT ENPGFGERVP G RVPGNLQP ...String:
MVAKSAALVV MGLSMASAFL APTPNNRASA QAPMKMAKSA ATKEFPFDDQ PGGVKWFPSS APYWDPLGFT NEKTEDEYWR IAHGEIKNG RLAMLAVTHY FVVGSGLRFP FKFGSVSTAD VPLGLGAIKA LPWAVWLQIA AFCLVLEVLT ENPGFGERVP G RVPGNLQP DTPSFNAPGD LEIRTKELNN ARLAMISIWG LWVGEIASGG VDPFTSFANW LKL

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Macromolecule #3: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 3 / Number of copies: 46 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #4: [(2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E})-17-[(4~{S},6~{R})...

MacromoleculeName: [(2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E})-17-[(4~{S},6~{R})-4-acetyloxy-2,2,6-trimethyl-6-oxidanyl-cyclohexylidene]-6,11,15-trimethyl-2-[(~{E})-2-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4- ...Name: [(2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E})-17-[(4~{S},6~{R})-4-acetyloxy-2,2,6-trimethyl-6-oxidanyl-cyclohexylidene]-6,11,15-trimethyl-2-[(~{E})-2-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]ethenyl]heptadeca-2,4,6,8,10,12,14,16-octaenyl] octanoate
type: ligand / ID: 4 / Number of copies: 6 / Formula: A1L1F
Molecular weightTheoretical: 785.102 Da

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Macromolecule #5: (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: 5 / Number of copies: 10 / 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 #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 68 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration5.0 mg/mL
BufferpH: 7.5 / Component - Concentration: 25.0 mM / Component - Formula: C8H18N2O4S / Component - Name: HEPES / Details: 0.002% LMNG
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Pressure: 10.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 16441 / Average exposure time: 3.0 sec. / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 6610197
CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 290174
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1rwt


Chain - Chain ID: B / Chain - Residue range: 14-229 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9mcc:
Cryo-EM structure of violaxanthin-chlorophyll-a-binding protein with red shifted Chl a (rVCP) from Trachydiscus minutus at 2.4 angstrom

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