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 5XWM | pdb_00005xwm

human ERp44 zinc-bound form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.214 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5XWM

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 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.

Macromolecule Content 

  • Total Structure Weight: 178.32 kDa 
  • Atom Count: 11,949 
  • Modeled Residue Count: 1,416 
  • Deposited Residue Count: 1,532 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Endoplasmic reticulum resident protein 44
A, B, C, D
383Homo sapiensMutation(s): 0 
Gene Names: ERP44, KIAA0573, TXNDC4, UNQ532/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
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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 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
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