5GU6

Crystal structure of Human ERp44 form I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of pH-dependent client binding by ERp44, a key regulator of protein secretion at the ER-Golgi interface

Watanabe, S.Harayama, M.Kanemura, S.Sitia, R.Inaba, K.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: E3224-E3232

  • DOI: 10.1073/pnas.1621426114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • ERp44 retrieves some endoplasmic reticulum (ER)-resident enzymes and immature oligomers of secretory proteins from the Golgi. Association of ERp44 with its clients is regulated by pH-dependent mechanisms, but the molecular details are not fully under ...

    ERp44 retrieves some endoplasmic reticulum (ER)-resident enzymes and immature oligomers of secretory proteins from the Golgi. Association of ERp44 with its clients is regulated by pH-dependent mechanisms, but the molecular details are not fully understood. Here we report high-resolution crystal structures of human ERp44 at neutral and weakly acidic pH. These structures reveal key regions in the C-terminal tail (C tail) missing in the original crystal structure, including a regulatory histidine-rich region and a subsequent extended loop. The former region forms a short α-helix (α16), generating a histidine-clustered site (His cluster). At low pH, the three Trx-like domains of ERp44 ("a," "b," and "b'") undergo significant rearrangements, likely induced by protonation of His157 located at the interface between the a and b domains. The α16-helix is partially unwound and the extended loop is disordered in weakly acidic conditions, probably due to electrostatic repulsion between the protonated histidines in the His cluster. Molecular dynamics simulations indicated that helix unwinding enhances the flexibility of the C tail, disrupting its normal hydrogen-bonding pattern. The observed pH-dependent conformational changes significantly enlarge the positively charged regions around the client-binding site of ERp44 at low pH. Mutational analyses showed that ERp44 forms mixed disulfides with specific cysteines residing on negatively charged loop regions of Ero1α. We propose that the protonation states of the essential histidines regulate the ERp44-client interaction by altering the C-tail dynamics and surface electrostatic potential of ERp44.


    Organizational Affiliation

    Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Tokyo 102-0076, Japan.,Vita-Salute San Raffaele University, 20132 Milan, Italy.,Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan; kinaba@tagen.tohoku.ac.jp.,Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan.,Unit of Protein Transport and Secretion, Division of Genetics and Cell Biology, Istituto Di Ricovero e Cura a Carattere Scientifico San Raffaele Scientific Institute, 20132 Milan, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endoplasmic reticulum resident protein 44
A
379Homo sapiensMutation(s): 0 
Gene Names: ERP44 (KIAA0573, TXNDC4)
Find proteins for Q9BS26 (Homo sapiens)
Go to Gene View: ERP44
Go to UniProtKB:  Q9BS26
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.204 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 81.630α = 90.00
b = 81.630β = 90.00
c = 139.910γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
Cootmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-05-03
    Type: Database references