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Basic information

Entry
Database: PDB / ID: 7ekq
TitleCrClpP-S2c
Components
  • (ATP-dependent Clp protease proteolytic ...) x 8
  • ATP-dependent Clp protease ATP-binding subunit CLPT4, chloroplastic
  • Chaperonin 11
  • Chaperonin 23
  • Cpn20 co-chaperonin subunit
KeywordsSTRUCTURAL PROTEIN / Clp / Complex / Protease / Chloroplast / Chlamydomnas
Function / homology
Function and homology information


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 / protein folding chaperone / chloroplast / unfolded protein 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 / protein folding chaperone / chloroplast / unfolded protein binding / protein-folding chaperone binding / ATPase binding / mitochondrial matrix / serine-type endopeptidase activity / ATP binding / metal ion binding
Similarity search - Function
Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. ...Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / Clp, N-terminal domain superfamily / GroES-like superfamily / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
ATP-dependent Clp protease proteolytic subunit / Uncharacterized protein / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease proteolytic subunit / Uncharacterized protein / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease ATP-binding subunit CLPT4, chloroplastic ...ATP-dependent Clp protease proteolytic subunit / Uncharacterized protein / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease proteolytic subunit / Uncharacterized protein / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease ATP-binding subunit CLPT4, chloroplastic / Uncharacterized protein / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWang, N. / Wang, Y.F. / Cong, Y. / Liu, C.M.
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, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: ATP-dependent Clp protease proteolytic subunit
B: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
H: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
J: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
M: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit
O: ATP-dependent Clp protease ATP-binding subunit CLPT4, chloroplastic
P: Chaperonin 11
Q: Chaperonin 23
R: Cpn20 co-chaperonin subunit
S: Cpn20 co-chaperonin subunit


Theoretical massNumber of molelcules
Total (without water)496,19119
Polymers496,19119
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ATP-dependent Clp protease proteolytic ... , 8 types, 14 molecules ABDFCEGHJMIKLN

#1: Protein ATP-dependent Clp protease proteolytic subunit / ClpR6 inactive subunit


Mass: 26571.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8INX1
#2: Protein ATP-dependent Clp protease proteolytic subunit / ClpP5 active subunit


Mass: 25815.459 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IL21, endopeptidase Clp
#3: Protein ATP-dependent Clp protease proteolytic subunit / ClpP4 active subunit


Mass: 33229.863 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IJ60, endopeptidase Clp
#4: Protein ATP-dependent Clp protease proteolytic subunit / Endopeptidase Clp / ClpP1c active subunit


Mass: 23105.768 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P42380, endopeptidase Clp
#5: Protein ATP-dependent Clp protease proteolytic subunit / ClpR1 inactive subunit


Mass: 28136.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3CXW8
#6: Protein ATP-dependent Clp protease proteolytic subunit / ClpR4 inactive subunit


Mass: 28381.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IXD6
#7: Protein ATP-dependent Clp protease proteolytic subunit / ClpR2 inactive subunit


Mass: 28345.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IS47
#8: Protein ATP-dependent Clp protease proteolytic subunit / ClpR3 inactive subunit


Mass: 43457.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IH07

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Protein , 4 types, 5 molecules OPQRS

#9: Protein ATP-dependent Clp protease ATP-binding subunit CLPT4, chloroplastic / ClpT4 subunit


Mass: 19869.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J353
#10: Protein Chaperonin 11 / Cpn11 co-chaperonin subunit


Mass: 10953.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J3C3
#11: Protein Chaperonin 23 / Cpn23 co-chaperonin subunit


Mass: 23061.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IJY7
#12: Protein Cpn20 co-chaperonin subunit


Mass: 20480.365 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DG79

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: complex of CrClp protease and co-chaperonin Cpn112023 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: YES
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
180 mMsodium chlorideNaCl1
220 mMTris baseTris-HCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 38 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49759 / Symmetry type: POINT

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