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- EMDB-31175: ClpP-S2 -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-31175
TitleClpP-S2
Map data
Sample
  • Complex: complex of CrClp protease and co-chaperonin Cpn112023
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWang N / Wang YF / Cong Y / Liu CM
CitationJournal: Nat Plants / Year: 2021
Title: The cryo-EM structure of the chloroplast ClpP complex.
Authors: Ning Wang / Yifan Wang / Qian Zhao / Xiang Zhang / Chao Peng / Wenjuan Zhang / Yanan Liu / Olivier Vallon / Michael Schroda / Yao Cong / Cuimin Liu /
Abstract: Protein homoeostasis in plastids is strategically regulated by the protein quality control system involving multiple chaperones and proteases, among them the Clp protease. Here, we determined the ...Protein homoeostasis in plastids is strategically regulated by the protein quality control system involving multiple chaperones and proteases, among them the Clp protease. Here, we determined the structure of the chloroplast ClpP complex from Chlamydomonas reinhardtii by cryo-electron microscopy. ClpP contains two heptameric catalytic rings without any symmetry. The top ring contains one ClpR6, three ClpP4 and three ClpP5 subunits while the bottom ring is composed of three ClpP1 subunits and one each of the ClpR1-4 subunits. ClpR3, ClpR4 and ClpT4 subunits connect the two rings and stabilize the complex. The chloroplast Cpn11/20/23 co-chaperonin, a co-factor of Cpn60, forms a cap on the top of ClpP by protruding mobile loops into hydrophobic clefts at the surface of the top ring. The co-chaperonin repressed ClpP proteolytic activity in vitro. By regulating Cpn60 chaperone and ClpP protease activity, the co-chaperonin may play a role in coordinating protein folding and degradation in the chloroplast.
History
DepositionApr 6, 2021-
Header (metadata) releaseOct 20, 2021-
Map releaseOct 20, 2021-
UpdateMay 4, 2022-
Current statusMay 4, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.852
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.852
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31175.png

Downloads & links

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Map

FileDownload / File: emd_31175.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 216 pix.
= 284.688 Å		1.32 Å/pix.
x 216 pix.
= 284.688 Å		1.32 Å/pix.
x 216 pix.
= 284.688 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.318 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.852 / Movie #1: 0.852
Minimum - Maximum-2.1053474 - 3.130598
Average (Standard dev.)0.016222265 (±0.16205128)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 284.688 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3181.3181.318
M x/y/z216216216
origin x/y/z0.0000.0000.000
length x/y/z284.688284.688284.688
α/β/γ90.00090.00090.000
start NX/NY/NZ336210602
NX/NY/NZ227193139
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS216216216
D min/max/mean-2.1053.1310.016

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Supplemental data

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Sample components

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Entire : complex of CrClp protease and co-chaperonin Cpn112023

EntireName: complex of CrClp protease and co-chaperonin Cpn112023
Components
  • Complex: complex of CrClp protease and co-chaperonin Cpn112023

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Supramolecule #1: complex of CrClp protease and co-chaperonin Cpn112023

SupramoleculeName: complex of CrClp protease and co-chaperonin Cpn112023 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

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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: 8
Component:
ConcentrationFormulaName
80.0 mMNaClsodium chloride
20.0 mMTris-HClTris base
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49759
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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