Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 58.19 kDa 
• Atom Count: 4,326 
• Modelled Residue Count: 521 
• Deposited Residue Count: 523 
• Unique protein chains: 1

 7A4V

Crystal structure of lid-truncated ADP-bound BiP in an oligomeric state

• PDB DOI:  https://doi.org/10.2210/pdb7A4V/pdb

• Classification: CHAPERONE
• Organism(s): Cricetulus griseus
• Expression System: Escherichia coli M15
• Mutation(s): Yes 


• Deposited: 2020-08-20 Released: 2020-12-16 
• Deposition Author(s): Perera, L.A., Ron, D.
• Funding Organization(s): Wellcome Trust

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.226 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Literature

Calcium depletion challenges endoplasmic reticulum proteostasis by destabilising BiP-substrate complexes.

Preissler, S., Rato, C., Yan, Y., Perera, L.A., Czako, A., Ron, D.

(2020) Elife 9

• PubMed: 33295873 
• DOI: https://doi.org/10.7554/eLife.62601
• Primary Citation of Related Structures:  
  6ZYH, 6ZYI, 6ZYJ, 7A4U, 7A4V


• PubMed Abstract: 
  

The metazoan endoplasmic reticulum (ER) serves both as a hub for maturation of secreted proteins and as an intracellular calcium storage compartment, facilitating calcium-release-dependent cellular processes. ER calcium depletion robustly activates the unfolded protein response (UPR). However, it is unclear how fluctuations in ER calcium impact organellar proteostasis. Here, we report that calcium selectively affects the dynamics of the abundant metazoan ER Hsp70 chaperone BiP, by enhancing its affinity for ADP. In the calcium-replete ER, ADP rebinding to post-ATP hydrolysis BiP-substrate complexes competes with ATP binding during both spontaneous and co-chaperone-assisted nucleotide exchange, favouring substrate retention. Conversely, in the calcium-depleted ER, relative acceleration of ADP-to-ATP exchange favours substrate release. These findings explain the rapid dissociation of certain substrates from BiP observed in the calcium-depleted ER and suggest a mechanism for tuning ER quality control and coupling UPR activity to signals that mobilise ER calcium in secretory cells.

---

Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoplasmic reticulum chaperone BiP	A	523	Cricetulus griseus	Mutation(s): 2  Gene Names: HSPA5, GRP78, I79_019946 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
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	E [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.226 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.179	α = 90
b = 51.249	β = 99.77
c = 118.801	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-16 
Deposition Author(s): Perera, L.A., Ron, D.

---

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	200848/Z/16/Z

Revision History  

• Version 1.0: 2020-12-16
  Type: Initial release