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Open data
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Basic information
Entry | Database: PDB / ID: 7ekq | ||||||
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Title | CrClpP-S2c | ||||||
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![]() | STRUCTURAL PROTEIN / Clp / Complex / Protease / Chloroplast / Chlamydomnas | ||||||
Function / homology | ![]() endopeptidase Clp / endopeptidase Clp complex / plastid / chloroplast stroma / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / chaperone cofactor-dependent protein refolding / chloroplast / unfolded protein binding / ATPase binding ...endopeptidase Clp / endopeptidase Clp complex / plastid / chloroplast stroma / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / chaperone cofactor-dependent protein refolding / chloroplast / unfolded protein binding / ATPase binding / protein-folding chaperone binding / mitochondrial matrix / serine-type endopeptidase activity / ATP hydrolysis activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
![]() | Wang, N. / Wang, Y.F. / Cong, Y. / Liu, C.M. | ||||||
![]() | ![]() 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 |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 617.9 KB | Display | ![]() |
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PDB format | ![]() | 501.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 961.6 KB | Display | ![]() |
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Full document | ![]() | 981.7 KB | Display | |
Data in XML | ![]() | 89.2 KB | Display | |
Data in CIF | ![]() | 137.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 31173MC ![]() 7ekoC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-ATP-dependent Clp protease proteolytic ... , 8 types, 14 molecules ABDFCEGHJMIKLN
#1: Protein | Mass: 26571.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||||||||
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#2: Protein | Mass: 25815.459 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 33229.863 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 23105.768 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | | Mass: 28136.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | | Mass: 28381.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | | Mass: 28345.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | | Mass: 43457.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 4 types, 5 molecules OPQRS
#9: Protein | Mass: 19869.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#10: Protein | Mass: 10953.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#11: Protein | Mass: 23061.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 20480.365 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: complex of CrClp protease and co-chaperonin Cpn112023 / Type: COMPLEX / Entity ID: all / Source: NATURAL | |||||||||||||||
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Molecular weight | Units: KILODALTONS/NANOMETER / Experimental value: YES | |||||||||||||||
Source (natural) | Organism: ![]() ![]() | |||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 38 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49759 / Symmetry type: POINT |