2Y1R | pdb_00002y1r

Structure of MecA121 & ClpC N-domain complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.258 (Depositor), 0.286 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.248 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Models: experimental
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Literature

Structure and Mechanism of the Hexameric Meca-Clpc Molecular Machine.

Wang, F.Mei, Z.Qi, Y.Yan, C.Hu, Q.Wang, J.Shi, Y.

(2011) Nature 471: 331

  • DOI: https://doi.org/10.1038/nature09780
  • Primary Citation Related Structures: 
    2Y1Q, 2Y1R, 3PXG, 3PXI

  • PubMed Abstract: 

    Regulated proteolysis by ATP-dependent proteases is universal in all living cells. Bacterial ClpC, a member of the Clp/Hsp100 family of AAA+ proteins (ATPases associated with diverse cellular activities) with two nucleotide-binding domains (D1 and D2), requires the adaptor protein MecA for activation and substrate targeting. The activated, hexameric MecA-ClpC molecular machine harnesses the energy of ATP binding and hydrolysis to unfold specific substrate proteins and translocate the unfolded polypeptide to the ClpP protease for degradation. Here we report three related crystal structures: a heterodimer between MecA and the amino domain of ClpC, a heterododecamer between MecA and D2-deleted ClpC, and a hexameric complex between MecA and full-length ClpC. In conjunction with biochemical analyses, these structures reveal the organizational principles behind the hexameric MecA-ClpC complex, explain the molecular mechanisms for MecA-mediated ClpC activation and provide mechanistic insights into the function of the MecA-ClpC molecular machine. These findings have implications for related Clp/Hsp100 molecular machines.


  • Organizational Affiliation
    • Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.

Macromolecule Content 

  • Total Structure Weight: 224.51 kDa 
  • Atom Count: 14,113 
  • Modeled Residue Count: 1,756 
  • Deposited Residue Count: 1,976 
  • Unique protein chains: 2

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NEGATIVE REGULATOR OF GENETIC COMPETENCE CLPC/MECB
A, B, C, D, E
A, B, C, D, E, F, G, H
149Bacillus subtilisMutation(s): 0 
UniProt
Find proteins for P37571 (Bacillus subtilis (strain 168))
Explore P37571 
Go to UniProtKB:  P37571
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37571
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ADAPTER PROTEIN MECA 1
I, J, K, L, M
I, J, K, L, M, N, O, P
98Bacillus subtilisMutation(s): 0 
UniProt
Find proteins for P37958 (Bacillus subtilis (strain 168))
Explore P37958 
Go to UniProtKB:  P37958
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37958
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SRT

Query on SRT



Download:Ideal Coordinates CCD File
AA [auth F]
BA [auth F]
CA [auth G]
DA [auth G]
EA [auth H]
AA [auth F],
BA [auth F],
CA [auth G],
DA [auth G],
EA [auth H],
FA [auth H],
Q [auth A],
R [auth A],
S [auth B],
T [auth B],
U [auth C],
V [auth C],
W [auth D],
X [auth D],
Y [auth E],
Z [auth E]
S,R MESO-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-XIXRPRMCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.258 (Depositor), 0.286 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.248 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.02α = 90
b = 124.72β = 90
c = 149.83γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-16
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-06-28
    Changes: Data collection
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description