1H8T

Echovirus 11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Determination of the Structure of a Decay Accelerating Factor-Binding Clinical Isolate of Echovirus 11 Allows Mapping of Mutants with Altered Receptor Requirements for Infection

Stuart, A.Mckee, T.Williams, P.A.Harley, C.Shen, S.Stuart, D.I.Brown, T.D.K.Lea, S.M.

(2002) J Virol 76: 7694

  • DOI: 10.1128/jvi.76.15.7694-7704.2002
  • Primary Citation of Related Structures:  
    1H8T

  • PubMed Abstract: 
  • We have used X-ray crystallography to determine the structure of a decay accelerating factor (DAF)-binding, clinic-derived isolate of echovirus 11 (EV11-207). The structures of the capsid proteins closely resemble those of capsid proteins of other picornaviruses ...

    We have used X-ray crystallography to determine the structure of a decay accelerating factor (DAF)-binding, clinic-derived isolate of echovirus 11 (EV11-207). The structures of the capsid proteins closely resemble those of capsid proteins of other picornaviruses. The structure allows us to interpret a series of amino acid changes produced by passaging EV11-207 in different cell lines as highlighting the locations of multiple receptor-binding sites on the virion surface. We suggest that a DAF-binding site is located at the fivefold axes of the virion, while the binding site for a distinct but as yet unidentified receptor is located within the canyon surrounding the virion fivefold axes.


    Organizational Affiliation

    Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ECHOVIRUS 11 COAT PROTEIN VP1A292Echovirus E11Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ECHOVIRUS 11 COAT PROTEIN VP2B262Echovirus E11Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ECHOVIRUS 11 COAT PROTEIN VP3C238Echovirus E11Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ECHOVIRUS 11 COAT PROTEIN VP4D68Echovirus E11Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYR
Query on MYR

Download Ideal Coordinates CCD File 
F [auth D]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
DOA
Query on DOA

Download Ideal Coordinates CCD File 
E [auth A]12-AMINO-DODECANOIC ACID
C12 H25 N O2
PBLZLIFKVPJDCO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 300.85α = 90
b = 300.85β = 90
c = 1476.62γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-11
    Type: Initial release
  • Version 1.1: 2012-01-11
    Changes: Derived calculations, Other, Refinement description, Version format compliance