4O8Q

Crystal structure of bovine MHD domain of the COPI delta subunit at 2.15 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the bovine COPI delta subunit mu homology domain at 2.15 angstrom resolution.

Lahav, A.Rozenberg, H.Parnis, A.Cassel, D.Adir, N.

(2015) Acta Crystallogr.,Sect.D 71: 1328-1334

  • DOI: 10.1107/S1399004715006203

  • PubMed Abstract: 
  • The heptameric COPI coat (coatomer) plays an essential role in vesicular transport in the early secretory system of eukaryotic cells. While the structures of some of the subunits have been determined, that of the δ-COP subunit has not been reported t ...

    The heptameric COPI coat (coatomer) plays an essential role in vesicular transport in the early secretory system of eukaryotic cells. While the structures of some of the subunits have been determined, that of the δ-COP subunit has not been reported to date. The δ-COP subunit is part of a subcomplex with structural similarity to tetrameric clathrin adaptors (APs), where δ-COP is the structural homologue of the AP μ subunit. Here, the crystal structure of the μ homology domain (MHD) of δ-COP (δ-MHD) obtained by phasing using a combined SAD-MR method is presented at 2.15 Å resolution. The crystallographic asymmetric unit contains two monomers that exhibit short sections of disorder, which may allude to flexible regions of the protein. The δ-MHD is composed of two subdomains connected by unstructured linkers. Comparison between this structure and those of known MHD domains from the APs shows significant differences in the positions of specific loops and β-sheets, as well as a more general change in the relative positions of the protein subdomains. The identified difference may be the major source of cargo-binding specificity. Finally, the crystal structure is used to analyze the potential effect of the I422T mutation in δ-COP previously reported to cause a neurodegenerative phenotype in mice.


    Organizational Affiliation

    Schulich Faculty of Chemistry, Technion, Haifa 32000, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coatomer subunit delta
A, B
245Bos taurusMutation(s): 0 
Gene Names: ARCN1 (COPD)
Find proteins for P53619 (Bos taurus)
Go to Gene View: ARCN1
Go to UniProtKB:  P53619
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.092α = 90.00
b = 110.333β = 90.00
c = 145.794γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
DNAdata collection
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-07
    Type: Initial release
  • Version 1.1: 2015-06-10
    Type: Database references
  • Version 1.2: 2015-06-24
    Type: Database references