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- PDB-1s6n: NMR Structure of Domain III of the West Nile Virus Envelope Prote... -

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Basic information

Entry
Database: PDB / ID: 1s6n
TitleNMR Structure of Domain III of the West Nile Virus Envelope Protein, Strain 385-99
Componentsenvelope glycoprotein
KeywordsVIRAL PROTEIN / BETA BARREL / FLAVIVIRUS
Function / homology
Function and homology information


membrane => GO:0016020 / host cell endoplasmic reticulum membrane / protein dimerization activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane
Similarity search - Function
Immunoglobulin-like - #350 / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set ...Immunoglobulin-like - #350 / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesWest Nile virus
MethodSOLUTION NMR
AuthorsVolk, D.E. / Beasley, D.W. / Kallick, D.A. / Holbrook, M.R. / Barrett, A.D. / Gorenstein, D.G.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Solution Structure and Antibody Binding Studies of the Envelope Protein Domain III from the New York Strain of West Nile Virus
Authors: Volk, D.E. / Beasley, D.W. / Kallick, D.A. / Holbrook, M.R. / Barrett, A.D. / Gorenstein, D.G.
#1: Journal: To be Published
Title: Letter to the Editor: 1H, 13C, and 15N resonance assignments for domain III of the West Nile Virus envelope protein
Authors: Volk, D.E. / Kallick, D.A. / Holbrook, M.R. / Beasley, D.W.C. / Barrett, A.D.T. / Gorenstein, D.G.
History
DepositionJan 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Remark 999SEQUENCE Residues 1-5 and 113-115 are not in the native sequence. They were added to increase solubility.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)12,1981
Polymers12,1981
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the least restraint violations
RepresentativeModel #1

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Components

#1: Protein envelope glycoprotein


Mass: 12197.809 Da / Num. of mol.: 1 / Fragment: Domain III
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) West Nile virus / Genus: Flavivirus / Strain: 385-99 / Plasmid: pMAL C2X / Production host: Escherichia coli (E. coli) / Strain (production host): C2X / References: UniProt: Q913C7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
1213D 13C-SEPARATED NOESY
NMR detailsText: CHEMICAL SHIFTS WERE DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY.

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Sample preparation

DetailsContents: 0.7MM WND3 PROTEIN, 50MM K2HPO4, 100MM NACL, 10MM NAN3, 0.1MM EDTA
Sample conditionsIonic strength: 50mM PHOSPHATE, 100mM NACL, 10mM NAN3 / pH: 6.8 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS7501
Varian UNITYPLUSVarianUNITYPLUS6002

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Processing

NMR software
NameVersionDeveloperClassification
AMBER6PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSON, SEIBEL,SINGH,WEINER,KOLLMANrefinement
VNMR6.1Bstructure solution
SANE1structure solution
FELIX98structure solution
AMBER6structure solution
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 15

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