5XWM

human ERp44 zinc-bound form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Zinc regulates ERp44-dependent protein quality control in the early secretory pathway.

Watanabe, S.Amagai, Y.Sannino, S.Tempio, T.Anelli, T.Harayama, M.Masui, S.Sorrentino, I.Yamada, M.Sitia, R.Inaba, K.

(2019) Nat Commun 10: 603-603

  • DOI: https://doi.org/10.1038/s41467-019-08429-1
  • Primary Citation of Related Structures:  
    5XWM

  • PubMed Abstract: 

    Zinc ions (Zn 2+ ) are imported into the early secretory pathway by Golgi-resident transporters, but their handling and functions are not fully understood. Here, we show that Zn 2+ binds with high affinity to the pH-sensitive chaperone ERp44, modulating its localization and ability to retrieve clients like Ero1α and ERAP1 to the endoplasmic reticulum (ER). Silencing the Zn 2+ transporters that uptake Zn 2+ into the Golgi led to ERp44 dysfunction and increased secretion of Ero1α and ERAP1. High-resolution crystal structures of Zn 2+ -bound ERp44 reveal that Zn 2+ binds to a conserved histidine-cluster. The consequent large displacements of the regulatory C-terminal tail expose the substrate-binding surface and RDEL motif, ensuring client capture and retrieval. ERp44 also forms Zn 2+ -bridged homodimers, which dissociate upon client binding. Histidine mutations in the Zn 2+ -binding sites compromise ERp44 activity and localization. Our findings reveal a role of Zn 2+ as a key regulator of protein quality control at the ER-Golgi interface.


  • Organizational Affiliation

    Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, 980-8577, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endoplasmic reticulum resident protein 44
A, B, C, D
383Homo sapiensMutation(s): 0 
Gene Names: ERP44KIAA0573TXNDC4UNQ532/PRO1075
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BS26 (Homo sapiens)
Explore Q9BS26 
Go to UniProtKB:  Q9BS26
PHAROS:  Q9BS26
GTEx:  ENSG00000023318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BS26
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
J [auth B]
K [auth B]
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B],
O [auth C],
P [auth C],
S [auth D],
T [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
M [auth B]
N [auth B]
Q [auth C]
H [auth A],
I [auth A],
M [auth B],
N [auth B],
Q [auth C],
R [auth C],
U [auth D],
V [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.15α = 90
b = 175.15β = 90
c = 407.81γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata processing
XSCALEdata scaling
SHELXDEphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-02
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references, Derived calculations