5C8C

Crystal structure of recombinant coxsackievirus A16 capsid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of Coxsackievirus A16 Capsids with Native Antigenicity: Implications for Particle Expansion, Receptor Binding, and Immunogenicity.

Ren, J.Wang, X.Zhu, L.Hu, Z.Gao, Q.Yang, P.Li, X.Wang, J.Shen, X.Fry, E.E.Rao, Z.Stuart, D.I.

(2015) J.Virol. 89: 10500-10511

  • DOI: 10.1128/JVI.01102-15
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Enterovirus 71 (EV71) and coxsackievirus A16 (CVA16) are the primary causes of the epidemics of hand-foot-and-mouth disease (HFMD) that affect more than a million children in China each year and lead to hundreds of deaths. Although there has been pro ...

    Enterovirus 71 (EV71) and coxsackievirus A16 (CVA16) are the primary causes of the epidemics of hand-foot-and-mouth disease (HFMD) that affect more than a million children in China each year and lead to hundreds of deaths. Although there has been progress with vaccines for EV71, the development of a CVA16 vaccine has proved more challenging, and the EV71 vaccine does not give useful cross-protection, despite the capsid proteins of the two viruses sharing about 80% sequence identity. The structural details of the expanded forms of the capsids, which possess nonnative antigenicity, are now well understood, but high resolution information for the native antigenic form of CVA16 has been missing. Here, we remedy this with high resolution X-ray structures of both mature and natural empty CVA16 particles and also of empty recombinant viruslike particles of CVA16 produced in insect cells, a potential vaccine antigen. All three structures are unexpanded native particles and antigenically identical. The recombinant particles have recruited a lipid moiety to stabilize the native antigenic state that is different from the one used in a natural virus infection. As expected, the mature CVA16 virus is similar to EV71; however, structural and immunogenic comparisons highlight differences that may have implications for vaccine production.


    Organizational Affiliation

    National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, China Sinovac Biotech Co., Ltd., Beijing, China.,National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, China Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing, China raozh@xtal.tsinghua.edu.cn dave@strubi.ox.ac.uk.,National Vaccine and Serum Institute, Beijing, China.,National Institutes for Food and Drug Control, No. 2, Tiantan Xili, Beijing, China.,National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, China.,Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, United Kingdom.,Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, United Kingdom Diamond Light Sources, Harwell Science and Innovation Campus, Didcot, United Kingdom raozh@xtal.tsinghua.edu.cn dave@strubi.ox.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VP1
A
297Coxsackievirus A16 (strain Tainan/5079/98)Mutation(s): 0 
Find proteins for Q9QF31 (Coxsackievirus A16 (strain Tainan/5079/98))
Go to UniProtKB:  Q9QF31
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VP0
B
323Coxsackievirus A16 (strain Tainan/5079/98)Mutation(s): 0 
Find proteins for Q9QF31 (Coxsackievirus A16 (strain Tainan/5079/98))
Go to UniProtKB:  Q9QF31
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
VP3
C
242Coxsackievirus A16 (strain Tainan/5079/98)Mutation(s): 0 
Find proteins for Q9QF31 (Coxsackievirus A16 (strain Tainan/5079/98))
Go to UniProtKB:  Q9QF31
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
STE
Query on STE

Download SDF File 
Download CCD File 
A
STEARIC ACID
C18 H36 O2
QIQXTHQIDYTFRH-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.164 
  • Space Group: P 42 3 2
Unit Cell:
Length (Å)Angle (°)
a = 347.900α = 90.00
b = 347.900β = 90.00
c = 347.900γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2015-10-07
    Type: Database references
  • Version 1.2: 2019-04-03
    Type: Data collection, Source and taxonomy