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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
ComponentsTICK-BORNE ENCEPHALITIS VIRUS GLYCOPROTEIN
KeywordsVIRAL PROTEIN / GLYCOPROTEIN / Viral protein
Function / homologyFlavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus glycoprotein E, immunoglobulin-like domain / mRNA cap 0/1 methyltransferase / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Immunoglobulin E-set / Genome polyprotein, Flavivirus / Helicase superfamily 1/2, ATP-binding domain / Flaviviral glycoprotein E, central domain, subdomain 2 / RNA-directed RNA polymerase, flavivirus ...Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus glycoprotein E, immunoglobulin-like domain / mRNA cap 0/1 methyltransferase / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Immunoglobulin E-set / Genome polyprotein, Flavivirus / Helicase superfamily 1/2, ATP-binding domain / Flaviviral glycoprotein E, central domain, subdomain 2 / RNA-directed RNA polymerase, flavivirus / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus non-structural protein NS2B / S-adenosyl-L-methionine-dependent methyltransferase / Flavivirus non-structural protein NS2A / Flavivirus capsid protein C / Flavivirus non-structural protein NS1 / Flaviviral glycoprotein E, central domain, subdomain 1 / Helicase, C-terminal / Flavivirus NS3, petidase S7 / Flavivirus polyprotein propeptide / Ribosomal RNA methyltransferase FtsJ domain / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flavivirus glycoprotein central and dimerisation domain / Flavivirus polyprotein propeptide / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus NS3 protease (NS3pro) domain profile. / Flavivirus NS2B domain profile. / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / RdRp of positive ssRNA viruses catalytic domain profile. / Flavivirus DEAD domain / Flavivirus glycoprotein, immunoglobulin-like domain / FtsJ-like methyltransferase / Flavivirus non-structural protein NS4A / Flaviviral glycoprotein E, dimerisation domain / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS2A / Flavivirus capsid protein C / Flavivirus RNA-directed RNA polymerase / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus non-structural Protein NS1 / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus polyprotein propeptide superfamily / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Envelope glycoprotein M superfamily, flavivirus / DEAD box, Flavivirus / Flavivirin / mRNA (guanine-N7-)-methyltransferase / mRNA (nucleoside-2'-O-)-methyltransferase / suppression by virus of host STAT2 activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / suppression by virus of host STAT1 activity / mRNA (guanine-N7-)-methyltransferase activity / host cell endoplasmic reticulum membrane / ATP-dependent helicase activity / host cell perinuclear region of cytoplasm / RNA helicase activity / double-stranded RNA binding / suppression by virus of host type I interferon-mediated signaling pathway / RNA helicase / nucleoside-triphosphatase / viral capsid / RNA-directed RNA polymerase / induction by virus of host autophagy / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / viral envelope / protein dimerization activity / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / serine-type endopeptidase activity / regulation of transcription, DNA-templated / transcription, DNA-templated / integral component of membrane / extracellular region / ATP binding / metal ion binding / Genome polyprotein
Function and homology information
Specimen sourceTick-borne encephalitis virus
MethodX-RAY DIFFRACTION / 1.9 Å resolution
AuthorsRey, F.A. / Harrison, S.C.
CitationJournal: Nature / Year: 1995
Title: The envelope glycoprotein from tick-borne encephalitis virus at 2 A resolution.
Authors: 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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Structure visualization

Structure viewerMolecule:
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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: Protein/peptide TICK-BORNE ENCEPHALITIS VIRUS GLYCOPROTEIN


Mass: 43231.145 Da / Num. of mol.: 1 / Source: (natural) Tick-borne encephalitis virus / Genus: Flavivirus / References: UniProt: P14336
#2: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 1 / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Water ChemComp-HOH / water


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

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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
pH: 8 / Method: unknown
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
12.5 M11KCl
230 %PEG300011
3Tris-HCl11

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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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