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- PDB-1z3r: Solution structure of the Omsk Hemhorraghic Fever Envelope Protei... -

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Basic information

Entry
Database: PDB / ID: 1z3r
TitleSolution structure of the Omsk Hemhorraghic Fever Envelope Protein Domain III
ComponentspolyproteinProteolysis
KeywordsVIRAL PROTEIN / Flavivirus Domain III / Omsk Hemorrhagic Fever / OHF / Envelope Protein
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 / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / 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 ...Immunoglobulin-like - #350 / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / 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
Envelope protein E / Envelope protein E
Similarity search - Component
Biological speciesOmsk hemorrhagic fever virus
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsVolk, D.E. / Chavez, L. / Beasley, D.W. / Barrett, A.D. / Gorenstein, D.G.
CitationJournal: Virology / Year: 2006
Title: Structure of the envelope protein domain III of Omsk hemorrhagic fever virus.
Authors: Volk, D.E. / Chavez, L. / Beasley, D.W. / Barrett, A.D. / Holbrook, M.R. / Gorenstein, D.G.
History
DepositionMar 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: polyprotein


Theoretical massNumber of molelcules
Total (without water)10,8451
Polymers10,8451
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 50structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein polyprotein / Proteolysis


Mass: 10845.471 Da / Num. of mol.: 1
Fragment: Omsk Hemorrhagic Fever Envelope Protein Domain III
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Omsk hemorrhagic fever virus / Genus: Flavivirus / Plasmid: pMal_c2x / Production host: Escherichia coli (E. coli) / References: UniProt: Q80J38, UniProt: Q80J37*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-separated NOESY
141

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Sample preparation

DetailsContents: Uniform (random) labeling with 15N / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100 mM NaCl 25 mM Tris-d11 / pH: 4.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS7501
Varian VXRSVarianVXRS6002

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Processing

NMR software
NameVersionDeveloperClassification
Felix2000Accelrys, Inc.processing
VNMR6.3Varian, Inc.collection
SANE04-04-27Duggan and Leggedata analysis
Amber6Case et al.structure solution
TALOS1Cornilescu, Delaglio and Baxrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 15

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