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- EMDB-9877: Structure of PSI dimer from Anabaena -

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Basic information

Database: EMDB / ID: EMD-9877
TitleStructure of PSI dimer from Anabaena
Map data
SamplePSI dimer
Biological speciesNostoc sp. PCC 7120 (Cyanobacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4 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 ReportSummary, Full report, XML, About validation report
DepositionApr 2, 2019-
Header (metadata) releaseNov 13, 2019-
Map releaseNov 13, 2019-
UpdateNov 13, 2019-
Current statusNov 13, 2019Processing site: PDBj / Status: Released

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
Supplemental images

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FileDownload / File: emd_9877.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.023889257 - 0.09283819
Average (Standard dev.)0.00030213883 (±0.0024929973)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
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
start NX/NY/NZ000
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0240.0930.000

Supplemental data

Sample components

Entire PSI dimer

EntireName: PSI dimer / Number of components: 1

Component #1: protein, PSI dimer

ProteinName: PSI dimer / Recombinant expression: No
MassTheoretical: 700 kDa
SourceSpecies: Nostoc sp. PCC 7120 (Cyanobacteria)

Experimental details

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 %

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)

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 117137
3D reconstructionSoftware: RELION / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

Atomic model buiding

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

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