5EJ0

The vaccinia virus H3 envelope protein, a major target of neutralizing antibodies, exhibits a glycosyltransferase fold and binds UDP-Glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Vaccinia Virus H3 Envelope Protein, a Major Target of Neutralizing Antibodies, Exhibits a Glycosyltransferase Fold and Binds UDP-Glucose.

Singh, K.Gittis, A.G.Gitti, R.K.Ostazeski, S.A.Su, H.P.Garboczi, D.N.

(2016) J Virol 90: 5020-5030

  • DOI: https://doi.org/10.1128/JVI.02933-15
  • Primary Citation of Related Structures:  
    5EJ0

  • PubMed Abstract: 

    The highly conserved H3 poxvirus protein is a major target of the human antibody response against poxviruses and is likely a key contributor to protection against infection. Here, we present the crystal structure of H3 from vaccinia virus at a 1.9-Å resolution. H3 looks like a glycosyltransferase, a family of enzymes that transfer carbohydrate molecules to a variety of acceptor substrates. Like glycosyltransferases, H3 binds UDP-glucose, as shown by saturation transfer difference (STD) nuclear magnetic resonance (NMR) spectroscopy, and this binding requires Mg(2+) Mutation of the glycosyltransferase-like metal ion binding motif in H3 greatly diminished its binding to UDP-glucose. We found by flow cytometry that H3 binds to the surface of human cells but does not bind well to cells that are deficient in surface glycosaminoglycans. STD NMR experiments using a heparin sulfate decasaccharide confirmed that H3 binds heparin sulfate. We propose that a surface of H3 with an excess positive charge may be the binding site for heparin. Heparin binding and glycosyltransferase activity may be involved in the function of H3 in the poxvirus life cycle.


  • Organizational Affiliation

    Structural Biology Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA ksingh@niaid.nih.gov dgarboczi@niaid.nih.gov.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope protein H3237Vaccinia virus WRMutation(s): 0 
Gene Names: VACWR101H3L
UniProt
Find proteins for P07240 (Vaccinia virus (strain Western Reserve))
Explore P07240 
Go to UniProtKB:  P07240
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07240
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG0
Query on PG0

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]
2-(2-METHOXYETHOXY)ETHANOL
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DHL
Query on DHL

Download Ideal Coordinates CCD File 
B [auth A]2-AMINO-ETHANETHIOL
C2 H7 N S
UFULAYFCSOUIOV-UHFFFAOYSA-N
PDO
Query on PDO

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A]
1,3-PROPANDIOL
C3 H8 O2
YPFDHNVEDLHUCE-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
POL
Query on POL

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I [auth A]N-PROPANOL
C3 H8 O
BDERNNFJNOPAEC-UHFFFAOYSA-N
EOH
Query on EOH

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Q [auth A],
R [auth A],
S [auth A]
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
MOH
Query on MOH

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T [auth A]
U [auth A]
V [auth A]
W [auth A]
X [auth A]
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A]
METHANOL
C H4 O
OKKJLVBELUTLKV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
Z [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.36α = 90
b = 54.79β = 90
c = 111.99γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2016-05-11
    Changes: Database references