Crystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with 2'-deoxy-ADP and inorganic phosphate

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

Starting Model: experimental
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Probing the ATP Site of GRP78 with Nucleotide Triphosphate Analogs.

Hughes, S.J.Antoshchenko, T.Chen, Y.Lu, H.Pizarro, J.C.Park, H.W.

(2016) PLoS One 11: e0154862-e0154862

  • DOI: https://doi.org/10.1371/journal.pone.0154862
  • Primary Citation of Related Structures:  
    5EVZ, 5EX5, 5EXW, 5EY4, 5F0X, 5F1X, 5F2R

  • PubMed Abstract: 

    GRP78, a member of the ER stress protein family, can relocate to the surface of cancer cells, playing key roles in promoting cell proliferation and metastasis. GRP78 consists of two major functional domains: the ATPase and protein/peptide-binding domains. The protein/peptide-binding domain of cell-surface GRP78 has served as a novel functional receptor for delivering cytotoxic agents (e.g., a apoptosis-inducing peptide or taxol) across the cell membrane. Here, we report our study on the ATPase domain of GRP78 (GRP78ATPase), whose potential as a transmembrane delivery system of cytotoxic agents (e.g., ATP-based nucleotide triphosphate analogs) remains unexploited. As the binding of ligands (ATP analogs) to a receptor (GRP78ATPase) is a pre-requisite for internalization, we determined the binding affinities and modes of GRP78ATPase for ADP, ATP and several ATP analogs using surface plasmon resonance and x-ray crystallography. The tested ATP analogs contain one of the following modifications: the nitrogen at the adenine ring 7-position to a carbon atom (7-deazaATP), the oxygen at the β-γ bridge position to a carbon atom (AMPPCP), or the removal of the 2'-OH group (2'-deoxyATP). We found that 7-deazaATP displays an affinity and a binding mode that resemble those of ATP regardless of magnesium ion (Mg++) concentration, suggesting that GRP78 is tolerant to modifications at the 7-position. By comparison, AMPPCP's binding affinity was lower than ATP and Mg++-dependent, as the removal of Mg++ nearly abolished binding to GRP78ATPase. The AMPPCP-Mg++ structure showed evidence for the critical role of Mg++ in AMPPCP binding affinity, suggesting that while GRP78 is sensitive to modifications at the β-γ bridge position, these can be tolerated in the presence of Mg++. Furthermore, 2'-deoxyATP's binding affinity was significantly lower than those for all other nucleotides tested, even in the presence of Mg++. The 2'-deoxyATP structure showed the conformation of the bound nucleotide flipped out of the active site, explaining the low affinity binding to GRP78 and suggesting that the 2'-OH group is essential for the high affinity binding to GRP78. Together, our results demonstrate that GRP78ATPase possesses nucleotide specificity more relaxed than previously anticipated and can tolerate certain modifications to the nucleobase 7-position and, to a lesser extent, the β-γ bridging atom, thereby providing a possible atomic mechanism underlying the transmembrane transport of the ATP analogs.

  • Organizational Affiliation

    Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5G 1L7, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
78 kDa glucose-regulated protein
A, B
400Homo sapiensMutation(s): 0 
Gene Names: HSPA5GRP78
UniProt & NIH Common Fund Data Resources
Find proteins for P11021 (Homo sapiens)
Explore P11021 
Go to UniProtKB:  P11021
GTEx:  ENSG00000044574 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11021
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on DTP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
C10 H16 N5 O12 P3
Query on DAT

Download Ideal Coordinates CCD File 
C10 H15 N5 O9 P2
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
O4 P
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.347α = 90
b = 74.448β = 97.67
c = 85.882γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-15
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description