5E84 | pdb_00005e84

ATP-bound state of BiP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 
    0.287 (Depositor), 0.285 (DCC) 
  • R-Value Work: 
    0.243 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 
    0.245 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5E84

Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1016/j.str.2015.10.012
  • Primary Citation Related Structures: 
    5E84, 5E85, 5E86

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 408.34 kDa 
  • Atom Count: 28,484 
  • Modeled Residue Count: 3,636 
  • Deposited Residue Count: 3,636 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
78 kDa glucose-regulated protein
A, B, C, D, E
A, B, C, D, E, F
606Homo sapiensMutation(s): 0 
Gene Names: HSPA5GRP78
EC: 3.6.4.10
UniProt & NIH Common Fund Data Resources
Find proteins for P11021 (Homo sapiens)
Explore P11021 
Go to UniProtKB:  P11021
PHAROS:  P11021
GTEx:  ENSG00000044574 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11021
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP

Query on ATP



Download:Ideal Coordinates CCD File
CA [auth D]
G [auth A]
KA [auth E]
O [auth B]
QA [auth F]
CA [auth D],
G [auth A],
KA [auth E],
O [auth B],
QA [auth F],
W [auth C]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
BA [auth C]
JA [auth D]
N [auth A]
PA [auth E]
V [auth B]
BA [auth C],
JA [auth D],
N [auth A],
PA [auth E],
V [auth B],
VA [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN

Query on ZN



Download:Ideal Coordinates CCD File
AA [auth C]
DA [auth D]
H [auth A]
HA [auth D]
IA [auth D]
AA [auth C],
DA [auth D],
H [auth A],
HA [auth D],
IA [auth D],
L [auth A],
M [auth A],
MA [auth E],
NA [auth E],
OA [auth E],
P [auth B],
Q [auth B],
RA [auth F],
TA [auth F],
U [auth B],
UA [auth F],
X [auth C],
Z [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
EA [auth D]
FA [auth D]
GA [auth D]
I [auth A]
J [auth A]
EA [auth D],
FA [auth D],
GA [auth D],
I [auth A],
J [auth A],
K [auth A],
LA [auth E],
R [auth B],
S [auth B],
SA [auth F],
T [auth B],
Y [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free:  0.287 (Depositor), 0.285 (DCC) 
  • R-Value Work:  0.243 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 0.245 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 222.468α = 90
b = 222.468β = 90
c = 209.46γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM098592, 1RO1GM109193

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Advisory, Author supporting evidence, Derived calculations
  • Version 1.2: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.3: 2023-09-27
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description