1KP8

Structural Basis for GroEL-assisted Protein Folding from the Crystal Structure of (GroEL-KMgATP)14 at 2.0 A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.243 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 1SX3


Literature

Structural Basis for GroEL-assisted Protein Folding from the Crystal Structure of (GroEL-KMgATP)14 at 2.0 A Resolution

Wang, J.Boisvert, D.C.

(2003) J Mol Biol 327: 843-855

  • DOI: 10.1016/s0022-2836(03)00184-0
  • Primary Citation of Related Structures:  
    1KP8

  • PubMed Abstract: 
  • Nucleotide regulates the affinity of the bacterial chaperonin GroEL for protein substrates. GroEL binds protein substrates with high affinity in the absence of ATP and with low affinity in its presence. We report the crystal structure of (GroEL-KMgATP)(1 ...

    Nucleotide regulates the affinity of the bacterial chaperonin GroEL for protein substrates. GroEL binds protein substrates with high affinity in the absence of ATP and with low affinity in its presence. We report the crystal structure of (GroEL-KMgATP)(14) refined to 2.0 A resolution in which the ATP triphosphate moiety is directly coordinated by both K(+) and Mg(2+). Upon the binding of KMgATP, we observe previously unnoticed domain rotations and a 102 degrees rotation of the apical domain surface helix I. Two major consequences are a large lateral displacement of, and a dramatic reduction of hydrophobicity in, the apical domain surface. These results provide a basis for the nucleotide-dependent regulation of protein substrate binding and suggest a mechanism for GroEL-assisted protein folding by forced unfolding.


    Related Citations: 
    • The 2.4 A Crystal Structure of the Bacterial Chaperonin GroEL Complexed with ATP Gamma S
      Boisvert, D.C., Wang, J., Otwinowski, Z., Horwich, A.L., Sigler, P.B.
      (1996) Nat Struct Biol 3: 170
    • The Crystal Structure of the Bacterial Chaperonin GroEL at 2.8 A
      Braig, K., Otwinowski, Z., Hegde, R., Boisvert, D.C., Joachimiak, A., Horwich, A.L., Sigler, P.B.
      (1994) Nature 371: 578
    • Conformational Variability in the Refined Structure of the Chaperonin GroEL at 2.8 A Resolution
      Braig, K., Adams, P.D., Brunger, A.T.
      (1995) Nat Struct Biol 2: 1083
    • The Crystal Structure of the Asymmetric GroEL-GroES-(ADP)7 Chaperonin Complex
      Xu, Z., Horwich, A.L., Sigler, P.B.
      (1997) Nature 388: 741

    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry Yale University, 266 Whitney Avenue, Bass Center, Room 418, New Haven, CT 06520-8114, USA. wang@mail.csb.yale.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
groEL proteinABCDEFGHABCDEFGHIJKLMN
547Escherichia coliMutation(s): 0 
Find proteins for P0A6F5 (Escherichia coli (strain K12))
Explore P0A6F5 
Go to UniProtKB:  P0A6F5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS

Download Ideal Coordinates CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A, B, C, E, F, G, H, J, K, L, M, N
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.243 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.571α = 90
b = 260.112β = 101.14
c = 150.2γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2001-12-30 
  • Released Date: 2003-03-25 
  • Deposition Author(s): Wang, J.
  • This entry supersedes: 1DER

Revision History 

  • Version 1.0: 2003-03-25
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2014-03-26
    Changes: Non-polymer description, Version format compliance
  • Version 1.4: 2017-10-11
    Changes: Refinement description