1QVR

Crystal Structure Analysis of ClpB

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.263 

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Literature

The Structure of ClpB: A Molecular Chaperone that Rescues Proteins from an Aggregated State

Lee, S., Sowa, M.E., Watanabe, Y., Sigler, P.B., Chiu, W., Yoshida, M., Tsai, F.T.F.

(2003) Cell 115: 229-240

  • DOI: 10.1016/s0092-8674(03)00807-9
  • Primary Citation of Related Structures:  
    1QVR

  • PubMed Abstract: 

    • Molecular chaperones assist protein folding by facilitating their "forward" folding and preventing aggregation. However, once aggregates have formed, these chaperones cannot facilitate protein disaggregation. Bacterial ClpB and its eukaryotic homolog Hsp104 are essential proteins of the heat-shock response, which have the remarkable capacity to rescue stress-damaged proteins from an aggregated state ...

    Molecular chaperones assist protein folding by facilitating their "forward" folding and preventing aggregation. However, once aggregates have formed, these chaperones cannot facilitate protein disaggregation. Bacterial ClpB and its eukaryotic homolog Hsp104 are essential proteins of the heat-shock response, which have the remarkable capacity to rescue stress-damaged proteins from an aggregated state. We have determined the structure of Thermus thermophilus ClpB (TClpB) using a combination of X-ray crystallography and cryo-electron microscopy (cryo-EM). Our single-particle reconstruction shows that TClpB forms a two-tiered hexameric ring. The ClpB/Hsp104-linker consists of an 85 A long and mobile coiled coil that is located on the outside of the hexamer. Our mutagenesis and biochemical data show that both the relative position and motion of this coiled coil are critical for chaperone function. Taken together, we propose a mechanism by which an ATP-driven conformational change is coupled to a large coiled-coil motion, which is indispensable for protein disaggregation.

    Organizational Affiliation: 

    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ClpB proteinA, B, C854Thermus thermophilusMutation(s): 0 
Gene Names: clpB
UniProt
Find proteins for Q9RA63 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q9RA63 
Go to UniProtKB:  Q9RA63
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RA63
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP
Download Ideal Coordinates CCD File 
EA [auth C],
FA [auth C],
L [auth A],
M [auth A],
V [auth B],
EA [auth C],
FA [auth C],
L [auth A],
M [auth A],
V [auth B],
W [auth B]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N		 Ligand Interaction
PT
Query on PT
Download Ideal Coordinates CCD File 
AA [auth C],
BA [auth C],
CA [auth C],
D [auth A],
DA [auth C],
AA [auth C],
BA [auth C],
CA [auth C],
D [auth A],
DA [auth C],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
X [auth C],
Y [auth C],
Z [auth C]
PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.263 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.747α = 90
b = 138.482β = 90
c = 212.215γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-21
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance