6EOF

Crystal structure of AMPylated GRP78 in ADP state

• PDB DOI:  https://doi.org/10.2210/pdb6EOF/pdb

• Classification: CHAPERONE
• Organism(s): Cricetulus griseus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-10-09 Released: 2017-11-01 
• Deposition Author(s): Yan, Y., Preissler, S., Read, R.J., Ron, D.
• Funding Organization(s): Wellcome Trust, British Heart Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.225 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 

Literature

AMPylation targets the rate-limiting step of BiP's ATPase cycle for its functional inactivation.

Preissler, S., Rohland, L., Yan, Y., Chen, R., Read, R.J., Ron, D.

(2017) Elife 6

• PubMed: 29064368 
• DOI: https://doi.org/10.7554/eLife.29428
• Primary Citation of Related Structures:  
  5O4P, 6EOB, 6EOC, 6EOE, 6EOF


• PubMed Abstract: 
  

The endoplasmic reticulum (ER)-localized Hsp70 chaperone BiP contributes to protein folding homeostasis by engaging unfolded client proteins in a process that is tightly coupled to ATP binding and hydrolysis. The inverse correlation between BiP AMPylation and the burden of unfolded ER proteins suggests a post-translational mechanism for adjusting BiP's activity to changing levels of ER stress, but the underlying molecular details are unexplored. We present biochemical and crystallographic studies indicating that irrespective of the identity of the bound nucleotide AMPylation biases BiP towards a conformation normally attained by the ATP-bound chaperone. AMPylation does not affect the interaction between BiP and J-protein co-factors but appears to allosterically impair J protein-stimulated ATP-hydrolysis, resulting in the inability of modified BiP to attain high affinity for its substrates. These findings suggest a molecular mechanism by which AMPylation serves as a switch to inactivate BiP, limiting its interactions with substrates whilst conserving ATP.

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Organizational Affiliation: 

Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 58.28 kDa 
• Atom Count: 4,156 
• Modelled Residue Count: 520 
• Deposited Residue Count: 522 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
78 kDa glucose-regulated protein	A	522	Cricetulus griseus	Mutation(s): 1  Gene Names: I79_019946, HSPA5, GRP78 EC: 3.6.4.10
UniProt
Find proteins for G3I8R9 (Cricetulus griseus) Explore G3I8R9  Go to UniProtKB:  G3I8R9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
AMP	D [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.225 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.047	α = 90
b = 75.61	β = 90
c = 97.5	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
AutoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-11-01 
Deposition Author(s): Yan, Y., Preissler, S., Read, R.J., Ron, D.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	082961/Z/07/Z
Wellcome Trust	United Kingdom	200848/Z/16/Z
British Heart Foundation	United Kingdom	PG/12/41/29679

Revision History  

• Version 1.0: 2017-11-01
  Type: Initial release