1TBW

Ligand Induced Conformational Shift in the N-terminal Domain of GRP94, Open Conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.259 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted AMPClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Ligand-induced Conformational Shift in the N-terminal Domain of GRP94, an Hsp90 Chaperone.

Immormino, R.M.Dollins, D.E.Shaffer, P.L.Soldano, K.L.Walker, M.A.Gewirth, D.T.

(2004) J Biol Chem 279: 46162-46171

  • DOI: https://doi.org/10.1074/jbc.M405253200
  • Primary Citation of Related Structures:  
    1TBW, 1TC0, 1TC6

  • PubMed Abstract: 

    GRP94 is the endoplasmic reticulum paralog of cytoplasmic Hsp90. Models of Hsp90 action posit an ATP-dependent conformational switch in the N-terminal ligand regulatory domain of the chaperone. However, crystal structures of the isolated N-domain of Hsp90 in complex with a variety of ligands have yet to demonstrate such a conformational change. We have determined the structure of the N-domain of GRP94 in complex with ATP, ADP, and AMP. Compared with the N-ethylcarboxamidoadenosine and radicicol-bound forms, these structures reveal a large conformational rearrangement in the protein. The nucleotide-bound form exposes new surfaces that interact to form a biochemically plausible dimer that is reminiscent of those seen in structures of MutL and DNA gyrase. Weak ATP binding and a conformational change in response to ligand identity are distinctive mechanistic features of GRP94 and suggest a model for how GRP94 functions in the absence of co-chaperones and ATP hydrolysis.


  • Organizational Affiliation

    Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endoplasmin
A, B
236Canis lupus familiarisMutation(s): 0 
Gene Names: TRA1
UniProt
Find proteins for P41148 (Canis lupus familiaris)
Explore P41148 
Go to UniProtKB:  P41148
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41148
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
H [auth B],
J [auth B],
K [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.259 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.202α = 90
b = 160.202β = 90
c = 109.564γ = 120
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted AMPClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-24
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-08-09
    Changes: Source and taxonomy
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations