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- EMDB-9700: Cryo-EM map of Chlamydomonas reinhardtii PSI-LHCI supercomplex at... -

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Entry
Database: EMDB / ID: 9700
TitleCryo-EM map of Chlamydomonas reinhardtii PSI-LHCI supercomplex at 6.9A resolution
Map dataC. reinhardtii PSI-LHCI supercomplex
SampleSupercomplex of photosystem I core with ten bound LHCA subunits.:
SourceChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / 6.9 Å resolution
AuthorsBurton-Smith RN / Kubota-Kawai H / Murata K
CitationJournal: J. Biol. Chem. / Year: 2019
Title: Ten antenna proteins are associated with the core in the supramolecular organization of the photosystem I supercomplex in .
Authors: Hisako Kubota-Kawai / Raymond N Burton-Smith / Ryutaro Tokutsu / Chihong Song / Seiji Akimoto / Makio Yokono / Yoshifumi Ueno / Eunchul Kim / Akimasa Watanabe / Kazuyoshi Murata / Jun Minagawa
Abstract: Photosystem I (PSI) is a large pigment-protein complex mediating light-driven charge separation and generating a highly negative redox potential, which is eventually utilized to produce organic ...Photosystem I (PSI) is a large pigment-protein complex mediating light-driven charge separation and generating a highly negative redox potential, which is eventually utilized to produce organic matter. In plants and algae, PSI possesses outer antennae, termed light-harvesting complex I (LHCI), which increase the energy flux to the reaction center. The number of outer antennae for PSI in the green alga is known to be larger than that of land plants. However, their exact number and location remain to be elucidated. Here, applying a newly established sample purification procedure, we isolated a highly pure PSI-LHCI supercomplex containing all nine LHCA gene products under state 1 conditions. Single-particle cryo-EM revealed the 3D structure of this supercomplex at 6.9 Å resolution, in which the densities near the PsaF and PsaJ subunits were assigned to two layers of LHCI belts containing eight LHCIs, whereas the densities between the PsaG and PsaH subunits on the opposite side of the LHCI belt were assigned to two extra LHCIs. Using single-particle cryo-EM, we also determined the 2D projection map of the mutant, which confirmed the assignment of LHCA2 and LHCA9 to the densities between PsaG and PsaH. Spectroscopic measurements of the PSI-LHCI supercomplex suggested that the bound LHCA2 and LHCA9 proteins have the ability to increase the light-harvesting energy for PSI. We conclude that the PSI in has a larger and more distinct outer-antenna organization and higher light-harvesting capability than that in land plants.
DateDeposition: Nov 2, 2018 / Header (metadata) release: Feb 27, 2019 / Map release: Feb 27, 2019 / Last update: Feb 27, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0516
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0516
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

Fileemd_9700.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.99 Å/pix.
= 509.952 Å
256 pix
1.99 Å/pix.
= 509.952 Å
256 pix
1.99 Å/pix.
= 509.952 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.992 Å
Density
Contour Level:0.0516 (by author), 0.0516 (movie #1):
Minimum - Maximum-0.07477446 - 0.3823998
Average (Standard dev.)0.0007578 (0.008599233)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.00.00.0
Limit255.0255.0255.0
Spacing256256256
CellA=B=C: 509.952 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.9921.9921.992
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z509.952509.952509.952
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ364364364
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0750.3820.001

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Supplemental data

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Sample components

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Entire Supercomplex of photosystem I core with ten bound LHCA subunits.

EntireName: Supercomplex of photosystem I core with ten bound LHCA subunits.
Number of components: 1

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Component #1: protein, Supercomplex of photosystem I core with ten bound LHCA s...

ProteinName: Supercomplex of photosystem I core with ten bound LHCA subunits.
Recombinant expression: No
MassTheoretical: 800 kDa
SourceSpecies: Chlamydomonas reinhardtii (plant) / Strain: 137c

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 %

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Electron microscopy imaging

ImagingMicroscope: JEOL 2200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: DIRECT ELECTRON DE-20 (5k x 3k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 10835
3D reconstructionSoftware: RELION / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: Correlation coefficient / Refinement space: REAL

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