6ASY

BiP-ATP2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Conformation transitions of the polypeptide-binding pocket support an active substrate release from Hsp70s.

Yang, J.Zong, Y.Su, J.Li, H.Zhu, H.Columbus, L.Zhou, L.Liu, Q.

(2017) Nat Commun 8: 1201-1201

  • DOI: 10.1038/s41467-017-01310-z

  • PubMed Abstract: 
  • Cellular protein homeostasis depends on heat shock proteins 70‚ÄČkDa (Hsp70s), a class of ubiquitous and highly conserved molecular chaperone. Key to the chaperone activity is an ATP-induced allosteric regulation of polypeptide substrate binding and re ...

    Cellular protein homeostasis depends on heat shock proteins 70‚ÄČkDa (Hsp70s), a class of ubiquitous and highly conserved molecular chaperone. Key to the chaperone activity is an ATP-induced allosteric regulation of polypeptide substrate binding and release. To illuminate the molecular mechanism of this allosteric coupling, here we present a novel crystal structure of an intact human BiP, an essential Hsp70 in ER, in an ATP-bound state. Strikingly, the polypeptide-binding pocket is completely closed, seemingly excluding any substrate binding. Our FRET, biochemical and EPR analysis suggests that this fully closed conformation is the major conformation for the ATP-bound state in solution, providing evidence for an active release of bound polypeptide substrates following ATP binding. The Hsp40 co-chaperone converts this fully closed conformation to an open conformation to initiate productive substrate binding. Taken together, this study provided a mechanistic understanding of the dynamic nature of the polypeptide-binding pocket in the Hsp70 chaperone cycle.


    Organizational Affiliation

    Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, VA, 23298, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
78 kDa glucose-regulated protein
A, B
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
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

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Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.159 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 75.829α = 62.05
b = 75.752β = 62.23
c = 78.791γ = 73.42
Software Package:
Software NamePurpose
SHELXDphasing
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction

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 StatesR01GM098592
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM109193
American Heart AssociationUnited States17GRNT33660506
Virginia Commonwealth UniversityUnited StatesBlick Scholar Award

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release