5E84

ATP-bound state of BiP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Close and Allosteric Opening of the Polypeptide-Binding Site in a Human Hsp70 Chaperone BiP.

Yang, J.Nune, M.Zong, Y.Zhou, L.Liu, Q.

(2015) Structure 23: 2191-2203

  • DOI: 10.1016/j.str.2015.10.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Binding immunoglobulin protein (BiP), an essential and ubiquitous Hsp70 chaperone in the ER, plays a key role in protein folding and quality control. BiP contains two functional domains: a nucleotide-binding domain (NBD) and a substrate-binding domai ...

    Binding immunoglobulin protein (BiP), an essential and ubiquitous Hsp70 chaperone in the ER, plays a key role in protein folding and quality control. BiP contains two functional domains: a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD). NBD binds and hydrolyzes ATP; the substrates for SBD are extended polypeptides. ATP binding allosterically accelerates polypeptide binding and release. Although crucial to the chaperone activity, the molecular mechanisms of polypeptide binding and allosteric coupling of BiP are poorly understood. Here, we present crystal structures of an intact human BiP in the ATP-bound state, the first intact eukaryotic Hsp70 structure, and isolated BiP-SBD with a peptide substrate bound representing the ADP-bound state. These structures and our biochemical analysis demonstrate that BiP has a unique NBD-SBD interface that is highly conserved only in eukaryotic Hsp70s found in the cytosol and ER to fortify its ATP-bound state and promote the opening of its polypeptide-binding pocket.


    Organizational Affiliation

    Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, VA 23298, USA.,Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, VA 23298, USA. Electronic address: qinglian.liu@vcuhealth.org.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
78 kDa glucose-regulated protein
A, B, C, D, E, F
606Homo sapiensMutation(s): 0 
Gene Names: HSPA5 (GRP78)
EC: 3.6.4.10
Find proteins for P11021 (Homo sapiens)
Go to Gene View: HSPA5
Go to UniProtKB:  P11021
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.243 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 222.468α = 90.00
b = 222.468β = 90.00
c = 209.460γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States1R01GM098592, 1RO1GM109193

Revision History 

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Advisory, Author supporting evidence, Derived calculations