6D28

Crystal Structure of the N-domain of the ER Hsp90 chaperone GRP94 in complex with the specific ligand NECA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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 Biol Chem 278: 48330-48338

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

  • 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, 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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EndoplasminA273Canis lupus familiarisMutation(s): 0 
Gene Names: HSP90B1GRP94TRA1
UniProt
Find proteins for P41148 (Canis lupus familiaris)
Explore P41148 
Go to UniProtKB:  P41148
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NEC (Subject of Investigation/LOI)
Query on NEC

Download Ideal Coordinates CCD File 
B [auth A]N-ETHYL-5'-CARBOXAMIDO ADENOSINE
C12 H16 N6 O4
JADDQZYHOWSFJD-FLNNQWSLSA-N
 Ligand Interaction
M2M
Query on M2M

Download Ideal Coordinates CCD File 
C [auth A]1-METHOXY-2-(2-METHOXYETHOXY)ETHANE
C6 H14 O3
SBZXBUIDTXKZTM-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
NEC BindingDB:  6D28 Kd: 200 (nM) from 1 assay(s)
Binding MOAD:  6D28 Kd: 200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.2α = 90
b = 99.18β = 90
c = 63.071γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA095130
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP01CA186866

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence