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- PDB-1svb: ENVELOPE GLYCOPROTEIN FROM TICK-BORNE ENCEPHALITIS VIRUS -

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Basic information

Entry
Database: PDB / ID: 1svb
TitleENVELOPE GLYCOPROTEIN FROM TICK-BORNE ENCEPHALITIS VIRUS
DescriptorTICK-BORNE ENCEPHALITIS VIRUS GLYCOPROTEIN
KeywordsVIRAL PROTEIN / GLYCOPROTEIN / Viral protein
Specimen sourceTick-borne encephalitis virus / virus / ダニ媒介脳炎ウイルス
MethodX-ray diffraction (1.9 Å resolution)
AuthorsRey, F.A. / Harrison, S.C.
CitationNature, 1995, 375, 291-298

Nature, 1995, 375, 291-298 Yorodumi Papers
The envelope glycoprotein from tick-borne encephalitis virus at 2 A resolution.
Rey, F.A. / Heinz, F.X. / Mandl, C. / Kunz, C. / Harrison, S.C.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 27, 1995 / Release: Jun 10, 1996
RevisionDateData content typeGroupProviderType
1.0Jun 10, 1996Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance

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Assembly

Deposited unit
A: TICK-BORNE ENCEPHALITIS VIRUS GLYCOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4522
Polyers43,2311
Non-polymers2211
Water7,278404
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)144.000, 144.000, 119.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP 61 2 2

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Components

#1: Polypeptide(L)TICK-BORNE ENCEPHALITIS VIRUS GLYCOPROTEIN


Mass: 43231.145 Da / Num. of mol.: 1
Source: (natural) Tick-borne encephalitis virus / virus / ダニ媒介脳炎ウイルス
References: UniProt: P14336

Cellular component

Molecular function

Biological process

  • clathrin-dependent endocytosis of virus by host cell (GO: 0075512)
  • fusion of virus membrane with host endosome membrane (GO: 0039654)
  • induction by virus of host autophagy (GO: 0039520)
  • regulation of transcription, DNA-templated (GO: 0006355)
  • suppression by virus of host STAT1 activity (GO: 0039563)
  • suppression by virus of host STAT2 activity (GO: 0039564)
  • suppression by virus of host type I interferon-mediated signaling pathway (GO: 0039502)
  • transcription, DNA-templated (GO: 0006351)
  • viral RNA genome replication (GO: 0039694)
  • virion attachment to host cell (GO: 0019062)
#2: ChemicalChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 1 / Formula: C8H15NO6
#3: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.12 / Density percent sol: 70.13
Crystal grow
*PLUS
Temp unit: K / pH: 8 / Method: unknown
Crystal grow comp
*PLUS

Crystal ID: 1 / Sol ID: 1

IDConcConc unitChemical formulaCommon name
12.5MKCl
230%PEG3000
3Tris-HCl

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionD resolution high: 1.9 Å / D resolution low: 2 Å / Number obs: 44584 / Observed criterion sigma I: 0
Reflection
*PLUS
Percent possible obs: 77.5 / Rmerge I obs: 0.108 / Redundancy: 4.8
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å / Percent possible obs: 22 / Rmerge I obs: 0.27 / Redundancy: 1.2 / MeanI over sigI obs: 2.3

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefineSigma F: 0
Least-squares processR factor R free: 0.224 / R factor R work: 0.183 / R factor obs: 0.183 / Highest resolution: 1.9 Å / Lowest resolution: 2 Å / Number reflection obs: 44584
Refine hist #LASTHighest resolution: 1.9 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 3028 / Nucleic acid: 0 / Ligand: 14 / Solvent: 404 / Total: 3446
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.632
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.18
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.273
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.18
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.273

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