6HA7

Crystal structure of the BiP NBD and MANF complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

MANF antagonizes nucleotide exchange by the endoplasmic reticulum chaperone BiP.

Yan, Y.Rato, C.Rohland, L.Preissler, S.Ron, D.

(2019) Nat Commun 10: 541-541

  • DOI: 10.1038/s41467-019-08450-4
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Despite its known role as a secreted neuroprotectant, much of the mesencephalic astrocyte-derived neurotrophic factor (MANF) is retained in the endoplasmic reticulum (ER) of producer cells. There, by unknown mechanisms, MANF plays a role in protein f ...

    Despite its known role as a secreted neuroprotectant, much of the mesencephalic astrocyte-derived neurotrophic factor (MANF) is retained in the endoplasmic reticulum (ER) of producer cells. There, by unknown mechanisms, MANF plays a role in protein folding homeostasis in complex with the ER-localized Hsp70 chaperone BiP. Here we report that the SAF-A/B, Acinus, and PIAS (SAP) domain of MANF selectively associates with the nucleotide binding domain (NBD) of ADP-bound BiP. In crystal structures the SAP domain engages the cleft between NBD subdomains Ia and IIa, stabilizing the ADP-bound conformation and clashing with the interdomain linker that occupies this site in ATP-bound BiP. MANF inhibits both ADP release from BiP and ATP binding to BiP, and thereby client release. Cells lacking MANF have fewer ER stress-induced BiP-containing high molecular weight complexes. These findings suggest that MANF contributes to protein folding homeostasis as a nucleotide exchange inhibitor that stabilizes certain BiP-client complexes.


    Organizational Affiliation

    Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endoplasmic reticulum chaperone BiP
A, B
387Cricetulus griseusMutation(s): 0 
Gene Names: HSPA5 (GRP78)
EC: 3.6.4.10
Find proteins for G3I8R9 (Cricetulus griseus)
Go to Gene View: HSPA5
Go to UniProtKB:  G3I8R9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Mesencephalic astrocyte-derived neurotrophic factor
C, D
158Mus musculusMutation(s): 0 
Gene Names: Manf (Armet)
Find proteins for Q9CXI5 (Mus musculus)
Go to UniProtKB:  Q9CXI5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.226 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 58.420α = 81.13
b = 60.960β = 88.33
c = 96.110γ = 74.33
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
Aimlessdata scaling
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-08-07 
  • Released Date: 2019-02-06 
  • Deposition Author(s): Yan, Y., Ron, D.

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom200848/Z/16/Z
Wellcome TrustUnited Kingdom100140

Revision History 

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2019-02-13
    Type: Data collection, Database references