1UPN | pdb_00001upn

COMPLEX OF ECHOVIRUS TYPE 12 WITH DOMAINS 3 AND 4 OF ITS RECEPTOR DECAY ACCELERATING FACTOR (CD55) BY CRYO ELECTRON MICROSCOPY AT 16 A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 16.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history

Literature

The Structure of Echovirus Type 12 Bound to a Two-Domain Fragment of its Cellular Attachment Protein Decay-Accelerating Factor (Cd 55)

Bhella, D.Goodfellow, I.G.Roversi, P.Pettigrew, D.Chaudhry, Y.Evans, D.J.Lea, S.M.

(2004) J Biological Chem 279: 8325

  • DOI: https://doi.org/10.1074/jbc.M311334200
  • Primary Citation Related Structures: 
    1UPN

  • PubMed Abstract: 

    Echovirus type 12 (EV12), an Enterovirus of the Picornaviridae family, uses the complement regulator decay-accelerating factor (DAF, CD55) as a cellular receptor. We have calculated a three-dimensional reconstruction of EV12 bound to a fragment of DAF consisting of short consensus repeat domains 3 and 4 from cryo-negative stain electron microscopy data (EMD code 1057). This shows that, as for an earlier reconstruction of the related echovirus type 7 bound to DAF, attachment is not within the viral canyon but occurs close to the 2-fold symmetry axes. Despite this general similarity our reconstruction reveals a receptor interaction that is quite different from that observed for EV7. Fitting of the crystallographic co-ordinates for DAF(34) and EV11 into the reconstruction shows a close agreement between the crystal structure of the receptor fragment and the density for the virus-bound receptor, allowing unambiguous positioning of the receptor with respect to the virion (PDB code 1UPN). Our finding that the mode of virus-receptor interaction in EV12 is distinct from that seen for EV7 raises interesting questions regarding the evolution and biological significance of the DAF binding phenotype in these viruses.


  • Organizational Affiliation
    • Medical Research Council Virology Unit, Church Street, Glasgow, G11 5JR, United Kingdom. d.bhella@vir.gla.ac.uk

Macromolecule Content 

  • Total Structure Weight: 109.34 kDa 
  • Atom Count: 7,463 
  • Modeled Residue Count: 964 
  • Deposited Residue Count: 990 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ECHOVIRUS 11 COAT PROTEIN VP1292Echovirus E11Mutation(s): 0 
UniProt
Find proteins for Q8JKE8 (Echovirus E11)
Explore Q8JKE8 
Go to UniProtKB:  Q8JKE8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8JKE8
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ECHOVIRUS 11 COAT PROTEIN VP2262Echovirus E11Mutation(s): 0 
UniProt
Find proteins for Q8JKE8 (Echovirus E11)
Explore Q8JKE8 
Go to UniProtKB:  Q8JKE8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8JKE8
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ECHOVIRUS 11 COAT PROTEIN VP3238Echovirus E11Mutation(s): 0 
UniProt
Find proteins for Q8JKE8 (Echovirus E11)
Explore Q8JKE8 
Go to UniProtKB:  Q8JKE8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8JKE8
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
ECHOVIRUS 11 COAT PROTEIN VP469Echovirus E11Mutation(s): 0 
UniProt
Find proteins for Q8JKE8 (Echovirus E11)
Explore Q8JKE8 
Go to UniProtKB:  Q8JKE8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8JKE8
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
COMPLEMENT DECAY-ACCELERATING FACTOR129Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P08174 (Homo sapiens)
Explore P08174 
Go to UniProtKB:  P08174
PHAROS:  P08174
GTEx:  ENSG00000196352 
Entity Groups
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UniProt GroupP08174
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 16.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONMRC IMAGE PROCESSING PACKAGE

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-07
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-04-19
    Changes: Other
  • Version 1.4: 2017-08-30
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary