4GB3

Human coxsackievirus B3 strain RD coat protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.339 
  • R-Value Work: 0.330 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Crystal Structure of a Coxsackievirus B3-RD Variant and a Refined 9-Angstrom Cryo-Electron Microscopy Reconstruction of the Virus Complexed with Decay-Accelerating Factor (DAF) Provide a New Footprint of DAF on the Virus Surface.

Yoder, J.D.Cifuente, J.O.Pan, J.Bergelson, J.M.Hafenstein, S.

(2012) J.Virol. 86: 12571-12581

  • DOI: 10.1128/JVI.01592-12
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The coxsackievirus-adenovirus receptor (CAR) and decay-accelerating factor (DAF) have been identified as cellular receptors for coxsackievirus B3 (CVB3). The first described DAF-binding isolate was obtained during passage of the prototype strain, Nan ...

    The coxsackievirus-adenovirus receptor (CAR) and decay-accelerating factor (DAF) have been identified as cellular receptors for coxsackievirus B3 (CVB3). The first described DAF-binding isolate was obtained during passage of the prototype strain, Nancy, on rhabdomyosarcoma (RD) cells, which express DAF but very little CAR. Here, the structure of the resulting variant, CVB3-RD, has been solved by X-ray crystallography to 2.74 Å, and a cryo-electron microscopy reconstruction of CVB3-RD complexed with DAF has been refined to 9.0 Å. This new high-resolution structure permits us to correct an error in our previous view of DAF-virus interactions, providing a new footprint of DAF that bridges two adjacent protomers. The contact sites between the virus and DAF clearly encompass CVB3-RD residues recently shown to be required for binding to DAF; these residues interact with DAF short consensus repeat 2 (SCR2), which is known to be essential for virus binding. Based on the new structure, the mode of the DAF interaction with CVB3 differs significantly from the mode reported previously for DAF binding to echoviruses.


    Organizational Affiliation

    The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
coat protein 1
1
281Coxsackievirus B3Mutation(s): 0 
Find proteins for F8VA14 (Coxsackievirus B3)
Go to UniProtKB:  F8VA14
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
coat protein 2
2
263Coxsackievirus B3Mutation(s): 0 
Find proteins for F8VA14 (Coxsackievirus B3)
Go to UniProtKB:  F8VA14
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
coat protein 3
3
238Coxsackievirus B3Mutation(s): 0 
Find proteins for F8VA14 (Coxsackievirus B3)
Go to UniProtKB:  F8VA14
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
coat protein 4
4
68Coxsackievirus B3Mutation(s): 0 
Find proteins for F8VA14 (Coxsackievirus B3)
Go to UniProtKB:  F8VA14
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYR
Query on MYR

Download SDF File 
Download CCD File 
4
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
PLM
Query on PLM

Download SDF File 
Download CCD File 
1
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.339 
  • R-Value Work: 0.330 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 296.638α = 90.00
b = 296.638β = 90.00
c = 813.215γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling
AMoREphasing
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-26
    Type: Initial release
  • Version 1.1: 2012-11-14
    Type: Database references