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- EMDB-9807: Structure of PSI tetramer from Anabaena -

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Basic information

Entry
Database: EMDB / ID: EMD-9807
TitleStructure of PSI tetramer from Anabaena
Map data
SamplePSI tetramer:
(Photosystem I ...) x 12 / (ligand) x 7
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / protein-chromophore linkage / electron transfer activity ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / 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 PsaK, reaction centre / Photosystem I PsaJ, reaction centre subunit IX / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Photosystem I, reaction centre subunit XI / Photosystem I protein PsaC / Photosystem I PsaX / Photosystem I PsaM, reaction centre / Electron transport accessory-like domain superfamily / Photosystem I PsaB / Photosystem I PsaA ...Photosystem I PsaK, reaction centre / Photosystem I PsaJ, reaction centre subunit IX / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Photosystem I, reaction centre subunit XI / Photosystem I protein PsaC / Photosystem I PsaX / Photosystem I PsaM, reaction centre / Electron transport accessory-like domain superfamily / Photosystem I PsaB / Photosystem I PsaA / Photosystem I PsaL, reaction centre subunit XI / Photosystem I PsaD / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit VIII / Photosystem I PsaA/PsaB, conserved site / Photosystem I PsaA/PsaB / Photosystem I PsaG/PsaK protein / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaX superfamily / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaA/PsaB superfamily / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site
Photosystem I reaction center subunit II / Photosystem I reaction center subunit PsaK 1 / Photosystem I reaction center subunit XI / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV / Photosystem I iron-sulfur center / Photosystem I reaction center subunit IX / Photosystem I 4.8 kDa protein / Photosystem I P700 chlorophyll a apoprotein A2 1 / Photosystem I reaction center subunit III ...Photosystem I reaction center subunit II / Photosystem I reaction center subunit PsaK 1 / Photosystem I reaction center subunit XI / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV / Photosystem I iron-sulfur center / Photosystem I reaction center subunit IX / Photosystem I 4.8 kDa protein / Photosystem I P700 chlorophyll a apoprotein A2 1 / Photosystem I reaction center subunit III / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit XII
Biological speciesNostoc sp. PCC 7120 (Cyanobacteria) / Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (Cyanobacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKato K / Nagao R / Shen JR / Miyazaki N / Akita F
CitationJournal: Nat Commun / Year: 2019
Title: Structure of a cyanobacterial photosystem I tetramer revealed by cryo-electron microscopy.
Authors: Koji Kato / Ryo Nagao / Tian-Yi Jiang / Yoshifumi Ueno / Makio Yokono / Siu Kit Chan / Mai Watanabe / Masahiko Ikeuchi / Jian-Ren Shen / Seiji Akimoto / Naoyuki Miyazaki / Fusamichi Akita /
Abstract: Photosystem I (PSI) functions to harvest light energy for conversion into chemical energy. The organisation of PSI is variable depending on the species of organism. Here we report the structure of a ...Photosystem I (PSI) functions to harvest light energy for conversion into chemical energy. The organisation of PSI is variable depending on the species of organism. Here we report the structure of a tetrameric PSI core isolated from a cyanobacterium, Anabaena sp. PCC 7120, analysed by single-particle cryo-electron microscopy (cryo-EM) at 3.3 Å resolution. The PSI tetramer has a C2 symmetry and is organised in a dimer of dimers form. The structure reveals interactions at the dimer-dimer interface and the existence of characteristic pigment orientations and inter-pigment distances within the dimer units that are important for unique excitation energy transfer. In particular, characteristic residues of PsaL are identified to be responsible for the formation of the tetramer. Time-resolved fluorescence analyses showed that the PSI tetramer has an enhanced excitation-energy quenching. These structural and spectroscopic findings provide insights into the physiological significance of the PSI tetramer and evolutionary changes of the PSI organisations.
Validation ReportPDB-ID: 6jeo

SummaryFull reportAbout validation report
History
DepositionFeb 6, 2019-
Header (metadata) releaseNov 13, 2019-
Map releaseNov 13, 2019-
UpdateNov 13, 2019-
Current statusNov 13, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6jeo
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9807.png

Downloads & links

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Map

FileDownload / File: emd_9807.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 440 pix.
= 492.8 Å		1.12 Å/pix.
x 440 pix.
= 492.8 Å		1.12 Å/pix.
x 440 pix.
= 492.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.12942305 - 0.26028016
Average (Standard dev.)0.00065376825 (±0.006231211)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 492.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.121.121.12
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z492.800492.800492.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-0.1290.2600.001

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Supplemental data

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Sample components

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Entire PSI tetramer

EntireName: PSI tetramer / Number of components: 20

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Component #1: protein, PSI tetramer

ProteinName: PSI tetramer / Recombinant expression: No
MassTheoretical: 1.44 MDa
SourceSpecies: Nostoc sp. PCC 7120 (Cyanobacteria)

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Component #2: protein, Photosystem I P700 chlorophyll a apoprotein A1

ProteinName: Photosystem I P700 chlorophyll a apoprotein A1 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 83.28968 kDa
SourceSpecies: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (Cyanobacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576

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Component #3: protein, Photosystem I P700 chlorophyll a apoprotein A2 1

ProteinName: Photosystem I P700 chlorophyll a apoprotein A2 1 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 83.457016 kDa
SourceSpecies: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (Cyanobacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576

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Component #4: protein, Photosystem I iron-sulfur center

ProteinName: Photosystem I iron-sulfur center / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 8.825206 kDa
SourceSpecies: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (Cyanobacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576

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Component #5: protein, Photosystem I reaction center subunit II

ProteinName: Photosystem I reaction center subunit II / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 15.17624 kDa
SourceSpecies: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (Cyanobacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576

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Component #6: protein, Photosystem I reaction center subunit IV

ProteinName: Photosystem I reaction center subunit IV / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 7.897051 kDa
SourceSpecies: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (Cyanobacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576

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Component #7: protein, Photosystem I reaction center subunit III

ProteinName: Photosystem I reaction center subunit III / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 17.850568 kDa
SourceSpecies: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (Cyanobacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576

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Component #8: protein, Photosystem I reaction center subunit VIII

ProteinName: Photosystem I reaction center subunit VIII / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 5.066925 kDa
SourceSpecies: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (Cyanobacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576

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Component #9: protein, Photosystem I reaction center subunit IX

ProteinName: Photosystem I reaction center subunit IX / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 5.499422 kDa
SourceSpecies: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (Cyanobacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576

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Component #10: protein, Photosystem I reaction center subunit PsaK 1

ProteinName: Photosystem I reaction center subunit PsaK 1 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 8.852457 kDa
SourceSpecies: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (Cyanobacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576

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Component #11: protein, Photosystem I reaction center subunit XI

ProteinName: Photosystem I reaction center subunit XI / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 18.130725 kDa
SourceSpecies: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (Cyanobacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576

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

ProteinName: Photosystem I reaction center subunit XII / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 4.42425 kDa
SourceSpecies: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (Cyanobacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576

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Component #13: protein, Photosystem I 4.8 kDa protein

ProteinName: Photosystem I 4.8 kDa protein / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 4.872792 kDa
SourceSpecies: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (Cyanobacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576

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Component #14: ligand, CHLOROPHYLL A ISOMER

LigandName: CHLOROPHYLL A ISOMER / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.893489 kDa

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Component #15: ligand, CHLOROPHYLL A

LigandName: CHLOROPHYLL A / Number of Copies: 376 / Recombinant expression: No
MassTheoretical: 0.893489 kDa

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Component #16: ligand, PHYLLOQUINONE

LigandName: PHYLLOQUINONEPhytomenadione / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 0.450696 kDa

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Component #17: ligand, IRON/SULFUR CLUSTER

LigandName: IRON/SULFUR CLUSTERIron–sulfur cluster / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 0.35164 kDa

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Component #18: ligand, BETA-CAROTENE

LigandName: BETA-CAROTENE / Number of Copies: 88 / Recombinant expression: No
MassTheoretical: 0.536873 kDa

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Component #19: ligand, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

LigandName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 0.72297 kDa

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Component #20: ligand, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

LigandName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.787158 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.014 mg/mL / pH: 6.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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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: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 111400
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Target criteria: Correlation coefficient / Refinement space: REAL
Input PDB model: 1JB0

1jb0

Output model

6jeo

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