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- EMDB-10995: Dunaliella Minimal Photosystem I -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-10995
TitleDunaliella Minimal Photosystem I
Map data
SampleLarge dunaliella salina photosystem I-LHC supercomplex
  • (Chlorophyll a-b binding protein, ...Light-harvesting complexes of green plants) x 2
  • Lhca2
  • Lhca4
  • (Photosystem I ...) x 4
  • PsaD
  • PsaE
  • PsaF
  • (ligand) x 12
Function / homology
Function and homology information


photosynthesis, light harvesting / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / protein-chromophore linkage ...photosynthesis, light harvesting / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / protein-chromophore linkage / electron transfer activity / magnesium ion binding / integral component of membrane / metal ion binding
Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I PsaJ, reaction centre subunit IX superfamily / Chlorophyll a/b binding domain superfamily / Chlorophyll A-B binding protein / Photosystem I PsaA/PsaB, conserved site / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Photosystem I protein PsaC ...Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I PsaJ, reaction centre subunit IX superfamily / Chlorophyll a/b binding domain superfamily / Chlorophyll A-B binding protein / Photosystem I PsaA/PsaB, conserved site / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA / Chlorophyll A-B binding protein, plant
Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Photosystem I P700 chlorophyll a apoprotein A2
Biological speciesDunaliella salina (plant) / Green alga (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsNelson N / Caspy I / Malavath T / Klaiman D / Shkolinsky Y
Funding support Israel, Belgium, 2 items
OrganizationGrant numberCountry
Israel Science Foundation569/17 Israel
European Research Council (ERC)723991 Belgium
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2020
Title: Structure and energy transfer pathways of the Dunaliella Salina photosystem I supercomplex.
Authors: Ido Caspy / Tirupathi Malavath / Daniel Klaiman / Maria Fadeeva / Yoel Shkolnisky / Nathan Nelson /
Abstract: Oxygenic photosynthesis evolved more than 3 billion years ago in cyanobacteria. The increased complexity of photosystem I (PSI) became apparent from the high-resolution structures that were obtained ...Oxygenic photosynthesis evolved more than 3 billion years ago in cyanobacteria. The increased complexity of photosystem I (PSI) became apparent from the high-resolution structures that were obtained for the complexes that were isolated from various organisms, ranging from cyanobacteria to plants. These complexes are all evolutionarily linked. In this paper, the researchers have uncovered the increased complexity of PSI in a single organism demonstrated by the coexistance of two distinct PSI compositions. The Large Dunaliella PSI contains eight additional subunits, six in PSI core and two light harvesting complexes. Two additional chlorophyll a molecules pertinent for efficient excitation energy transfer in state II transition were identified in PsaL and PsaO. Short distances between these newly identified chlorophylls correspond with fast excitation transfer rates previously reported during state II transition. The apparent PSI conformations could be a coping mechanism for the high salinity.
Validation ReportPDB-ID: 6yxr

SummaryFull reportAbout validation report
History
DepositionMay 3, 2020-
Header (metadata) releaseJul 1, 2020-
Map releaseJul 1, 2020-
UpdateJul 22, 2020-
Current statusJul 22, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6yxr
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10995.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 384.12 Å
1.07 Å/pix.
x 360 pix.
= 384.12 Å
1.07 Å/pix.
x 360 pix.
= 384.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.05646487 - 0.12832023
Average (Standard dev.)0.00011159403 (±0.0038285782)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 384.12003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0671.0671.067
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z384.120384.120384.120
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ250250250
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0560.1280.000

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Supplemental data

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Half map: #1

Fileemd_10995_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_10995_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Large dunaliella salina photosystem I-LHC supercomplex

EntireName: Large dunaliella salina photosystem I-LHC supercomplex
Number of components: 24

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Component #1: protein, Large dunaliella salina photosystem I-LHC supercomplex

ProteinName: Large dunaliella salina photosystem I-LHC supercomplex
Recombinant expression: No
SourceSpecies: Dunaliella salina (plant)

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Component #2: protein, Chlorophyll a-b binding protein, chloroplastic

ProteinName: Chlorophyll a-b binding protein, chloroplastic / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.30523 kDa
SourceSpecies: Green alga (plant)

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Component #3: protein, Lhca2

ProteinName: Lhca2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.813822 kDa
SourceSpecies: Dunaliella salina (plant)

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

ProteinName: Chlorophyll a-b binding protein, chloroplastic / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.732824 kDa
SourceSpecies: Green alga (plant)

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Component #5: protein, Lhca4

ProteinName: Lhca4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.131031 kDa
SourceSpecies: Dunaliella salina (plant)

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Component #6: protein, Photosystem I P700 chlorophyll a apoprotein A1

ProteinName: Photosystem I P700 chlorophyll a apoprotein A1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 81.748172 kDa
SourceSpecies: Green alga (plant)

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Component #7: protein, Photosystem I P700 chlorophyll a apoprotein A2

ProteinName: Photosystem I P700 chlorophyll a apoprotein A2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 81.327992 kDa
SourceSpecies: Green alga (plant)

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Component #8: protein, Photosystem I iron-sulfur center

ProteinName: Photosystem I iron-sulfur center / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.71709 kDa
SourceSpecies: Green alga (plant)

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Component #9: protein, PsaD

ProteinName: PsaD / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.883294 kDa
SourceSpecies: Dunaliella salina (plant)

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Component #10: protein, PsaE

ProteinName: PsaE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.297158 kDa
SourceSpecies: Dunaliella salina (plant)

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Component #11: protein, PsaF

ProteinName: PsaF / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.212902 kDa
SourceSpecies: Dunaliella salina (plant)

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Component #12: protein, Photosystem I reaction center subunit IX

ProteinName: Photosystem I reaction center subunit IX / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.467188 kDa
SourceSpecies: Green alga (plant)

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Component #13: ligand, (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-...

LigandName: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.568871 kDa

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Component #14: ligand, (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRA...

LigandName: (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
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.60087 kDa

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Component #15: ligand, BETA-CAROTENE

LigandName: BETA-CAROTENE / Number of Copies: 23 / Recombinant expression: No
MassTheoretical: 0.536873 kDa

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Component #16: ligand, CHLOROPHYLL A

LigandName: CHLOROPHYLL A / Number of Copies: 134 / Recombinant expression: No
MassTheoretical: 0.893489 kDa

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Component #17: ligand, CHLOROPHYLL B

LigandName: CHLOROPHYLL B / Number of Copies: 10 / Recombinant expression: No
MassTheoretical: 0.907472 kDa

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Component #18: ligand, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

LigandName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.72297 kDa

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Component #19: ligand, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

LigandName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 0.787158 kDa

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Component #20: ligand, 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

LigandName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.704998 kDa

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Component #21: ligand, CHLOROPHYLL A ISOMER

LigandName: CHLOROPHYLL A ISOMER / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.893489 kDa

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Component #22: ligand, PHYLLOQUINONE

LigandName: PHYLLOQUINONEPhytomenadione / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.450696 kDa

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Component #23: ligand, IRON/SULFUR CLUSTER

LigandName: IRON/SULFUR CLUSTERIron–sulfur cluster / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.35164 kDa

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Component #24: ligand, DIGALACTOSYL DIACYL GLYCEROL (DGDG)

LigandName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.949299 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 % / Details: 2.5 sec blotting before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 42.68 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Defocus: 900.0 - 3000.0 nm
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 4306

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 45969
3D reconstructionSoftware: RELION / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Output model

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