5LZ6

Crystal structure of human ACBD3 GOLD domain in complex with 3A protein of Aichivirus B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Kobuviral Non-structural 3A Proteins Act as Molecular Harnesses to Hijack the Host ACBD3 Protein.

Klima, M.Chalupska, D.Rozycki, B.Humpolickova, J.Rezabkova, L.Silhan, J.Baumlova, A.Dubankova, A.Boura, E.

(2017) Structure 25: 219-230

  • DOI: 10.1016/j.str.2016.11.021
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Picornaviruses are small positive-sense single-stranded RNA viruses that include many important human pathogens. Within the host cell, they replicate at specific replication sites called replication organelles. To create this membrane platform, they ...

    Picornaviruses are small positive-sense single-stranded RNA viruses that include many important human pathogens. Within the host cell, they replicate at specific replication sites called replication organelles. To create this membrane platform, they hijack several host factors including the acyl-CoA-binding domain-containing protein-3 (ACBD3). Here, we present a structural characterization of the molecular complexes formed by the non-structural 3A proteins from two species of the Kobuvirus genus of the Picornaviridae family and the 3A-binding domain of the host ACBD3 protein. Specifically, we present a series of crystal structures as well as a molecular dynamics simulation of the 3A:ACBD3 complex at the membrane, which reveals that the viral 3A proteins act as molecular harnesses to enslave the ACBD3 protein leading to its stabilization at target membranes. Our data provide a structural rationale for understanding how these viral-host protein complexes assemble at the atomic level and identify new potential targets for antiviral therapies.


    Organizational Affiliation

    Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague, Czech Republic. Electronic address: klima@uochb.cas.cz.,Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland.,Institute of Physics, Polish Academy of Sciences, 02-668 Warsaw, Poland.,Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague, Czech Republic.,Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague, Czech Republic. Electronic address: boura@uochb.cas.cz.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Golgi resident protein GCP60
A
166Homo sapiensMutation(s): 0 
Gene Names: ACBD3 (GCP60, GOCAP1, GOLPH1)
Find proteins for Q9H3P7 (Homo sapiens)
Go to Gene View: ACBD3
Go to UniProtKB:  Q9H3P7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
3A
B
38Aichivirus BMutation(s): 0 
Find proteins for Q8BES6 (Aichivirus B)
Go to UniProtKB:  Q8BES6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download SDF File 
Download CCD File 
A
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.215 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 55.630α = 90.00
b = 55.630β = 90.00
c = 144.270γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-09-29 
  • Released Date: 2016-12-14 
  • Deposition Author(s): Klima, M., Boura, E.

Revision History 

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2017-12-13
    Type: Database references