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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-31171 | |||||||||
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Title | CrClpP-S1 | |||||||||
![]() | the 3.3 angstrom resolution cryo-EM density map of CrClp protease complex in Chlamydomonas reinhardtii. | |||||||||
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![]() | Clp / Complex / Protease / Chloroplast / Chlamydomnas / Atp-dependent. / STRUCTURAL PROTEIN | |||||||||
Function / homology | ![]() endopeptidase Clp / endopeptidase Clp complex / plastid / ATP-dependent peptidase activity / chloroplast stroma / protein quality control for misfolded or incompletely synthesized proteins / chloroplast / ATPase binding / serine-type endopeptidase activity Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Wang N / Wang YF | |||||||||
![]() | ![]() 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
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 4.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.6 KB 18.6 KB | Display Display | ![]() |
Images | ![]() | 93.2 KB | ||
Filedesc metadata | ![]() | 6.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 406.2 KB | Display | ![]() |
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Full document | ![]() | 405.7 KB | Display | |
Data in XML | ![]() | 5.8 KB | Display | |
Data in CIF | ![]() | 6.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ekoMC ![]() 7ekqC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | the 3.3 angstrom resolution cryo-EM density map of CrClp protease complex in Chlamydomonas reinhardtii. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.318 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : complex of CrClp protease
+Supramolecule #1: complex of CrClp protease
+Macromolecule #1: ATP-dependent Clp protease proteolytic subunit
+Macromolecule #2: ATP-dependent Clp protease proteolytic subunit
+Macromolecule #3: ATP-dependent Clp protease proteolytic subunit
+Macromolecule #4: ATP-dependent Clp protease proteolytic subunit
+Macromolecule #5: ATP-dependent Clp protease proteolytic subunit
+Macromolecule #6: ATP-dependent Clp protease proteolytic subunit
+Macromolecule #7: ATP-dependent Clp protease proteolytic subunit
+Macromolecule #8: ATP-dependent Clp protease proteolytic subunit
+Macromolecule #9: ATP-dependent Clp protease ATP-binding subunit CLPT4, chloroplastic
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 Component:
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 38.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 131245 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |