1QYE | pdb_00001qye

Crystal Structure of the N-domain of the ER Hsp90 chaperone GRP94 in complex with 2-chlorodideoxyadenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.272 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structure of the N-terminal Domain of GRP94. Basis for Ligand Specificity and Regulation

Soldano, K.L.Jivan, A.Nicchitta, C.V.Gewirth, D.T.

(2003) J Biological Chem 278: 48330-48338

  • DOI: https://doi.org/10.1074/jbc.M308661200
  • Primary Citation Related Structures: 
    1QY8, 1QYE, 1U2O, 6D28

  • PubMed Abstract: 

    GRP94, the endoplasmic reticulum (ER) paralog of the chaperone Hsp90, plays an essential role in the structural maturation or secretion of a subset of proteins destined for transport to the cell surface, such as the Toll-like receptors 2 and 4, and IgG, respectively. GRP94 differs from cytoplasmic Hsp90 by exhibiting very weak ATP binding and hydrolysis activity. GRP94 also binds selectively to a series of substituted adenosine analogs. The high resolution crystal structures at 1.75-2.1 A of the N-terminal and adjacent charged domains of GRP94 in complex with N-ethylcarboxamidoadenosine, radicicol, and 2-chlorodideoxyadenosine reveals a structural mechanism for ligand discrimination among hsp90 family members. The structures also identify a putative subdomain that may act as a ligand-responsive switch. The residues of the charged region fold into a disordered loop whose termini are ordered and continue the twisted beta sheet that forms the structural core of the N-domain. This continuation of the beta sheet past the charged domain suggests a structural basis for the association of the N-terminal and middle domains of the full-length chaperone.


  • Organizational Affiliation
    • Departments of Biochemistry and Cell Biology, Duke University Medical Center, Durham, North Carolina 27710, USA.

Macromolecule Content 

  • Total Structure Weight: 31.05 kDa 
  • Atom Count: 2,045 
  • Modeled Residue Count: 225 
  • Deposited Residue Count: 269 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Endoplasmin269Canis lupus familiarisMutation(s): 0 
Gene Names: TRA1
EC: 3.6.4
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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDY

Query on CDY



Download:Ideal Coordinates CCD File
B [auth A]2-CHLORODIDEOXYADENOSINE
C10 H12 Cl N5 O2
FNLILOONPKMGST-NTSWFWBYSA-N
M2M

Query on M2M



Download:Ideal Coordinates CCD File
C [auth A]1-METHOXY-2-(2-METHOXYETHOXY)ETHANE
C6 H14 O3
SBZXBUIDTXKZTM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.272 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.008α = 90
b = 98.974β = 90
c = 63.254γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description