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

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Basic information

Entry
Database: EMDB / ID: EMD-9700
TitleCryo-EM map of Chlamydomonas reinhardtii PSI-LHCI supercomplex at 6.9A resolution
Map dataC. reinhardtii PSI-LHCI supercomplex
Sample
  • Complex: Supercomplex of photosystem I core with ten bound LHCA subunits.
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.9 Å
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 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.
History
DepositionNov 2, 2018-
Header (metadata) releaseFeb 27, 2019-
Map releaseFeb 27, 2019-
UpdateApr 10, 2019-
Current statusApr 10, 2019Processing site: PDBj / Status: Released

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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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9700.png

Downloads & links

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Map

FileDownload / File: emd_9700.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC. reinhardtii PSI-LHCI supercomplex
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0516 / Movie #1: 0.0516
Minimum - Maximum-0.07477446 - 0.3823998
Average (Standard dev.)0.0007578 (±0.008599233)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 509.952 Å
α=β=γ: 90.0 °

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
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.
Components
  • Complex: Supercomplex of photosystem I core with ten bound LHCA subunits.

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Supramolecule #1: Supercomplex of photosystem I core with ten bound LHCA subunits.

SupramoleculeName: Supercomplex of photosystem I core with ten bound LHCA subunits.
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: 137c
Molecular weightTheoretical: 800 KDa

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL 2200FS
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

CTF correctionSoftware - Name: CTFFIND
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5l8r

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 10835
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationSoftware - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient

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