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- PDB-3vtt: High Resolution crystal structure of Dengue 3 Envelope protein do... -

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Basic information

Entry
Database: PDB / ID: 3vtt
TitleHigh Resolution crystal structure of Dengue 3 Envelope protein domain III (ED3)
ComponentsEnvelope protein E
KeywordsVIRAL PROTEIN / STRUCTURAL PROTEIN / immunoglobin like domain / Epitope presentation / cellular attachment
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / : / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / : / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Immunoglobulin-like - #350 / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus ...Immunoglobulin-like - #350 / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / 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 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesDengue virus type 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsElahi, M. / Islam, M.M. / Kuroda, Y.
CitationJournal: Proteins / Year: 2013
Title: High resolution crystal structure of dengue-3 envelope protein domain III suggests possible molecular mechanisms for serospecific antibody recognition
Authors: Elahi, M. / Islam, M.M. / Noguchi, K. / Yohda, M. / Kuroda, Y.
History
DepositionJun 7, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope protein E
B: Envelope protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4394
Polymers23,2472
Non-polymers1922
Water2,630146
1
A: Envelope protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7192
Polymers11,6231
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Envelope protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7192
Polymers11,6231
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.03, 37.68, 52.54
Angle α, β, γ (deg.)90.00, 105.03, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE BIOLOGICAL ASSEMBLY OF THE DOMAIN IS TO BE INVESTIGATED.

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Components

#1: Protein Envelope protein E /


Mass: 11623.287 Da / Num. of mol.: 2 / Fragment: UNP residues 574-678
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus type 3 / Strain: Philippines/H87/1956 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 DE3PlysS / References: UniProt: P27915
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 4000, 0.2M Lithium sulfate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 16, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→30.255 Å / Num. all: 21277 / Num. obs: 21522 / % possible obs: 99 % / Observed criterion σ(F): 1.37 / Observed criterion σ(I): 1.37 / Redundancy: 2.8 % / Biso Wilson estimate: 23.64 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.034 / Net I/σ(I): 2.31

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPAuto MRphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→30.255 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.8328 / SU ML: 0.39 / σ(F): 1.37 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2554 1092 5.14 %
Rwork0.2057 --
obs0.2083 21261 99.01 %
all-21522 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.257 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso max: 85.88 Å2 / Biso mean: 33.1108 Å2 / Biso min: 10.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.1565 Å20 Å2-0.1208 Å2
2--0.4109 Å20 Å2
3----0.2544 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1559 0 10 146 1715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071611
X-RAY DIFFRACTIONf_angle_d1.1452176
X-RAY DIFFRACTIONf_dihedral_angle_d13.998608
X-RAY DIFFRACTIONf_chiral_restr0.077242
X-RAY DIFFRACTIONf_plane_restr0.004279
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7002-1.77760.35911400.28452438257898
1.7776-1.87130.28641340.239325342668100
1.8713-1.98860.28251270.2192512263999
1.9886-2.14210.24761370.214825182655100
2.1421-2.35750.2711410.21332535267699
2.3575-2.69850.27181280.21472529265799
2.6985-3.39910.23281460.20472535268199
3.3991-30.25970.24141390.18442568270798
Refinement TLS params.Method: refined / Origin x: -18.3256 Å / Origin y: 0.0971 Å / Origin z: 14.4097 Å
111213212223313233
T0.1364 Å20.056 Å20.0212 Å2-0.1621 Å20.0477 Å2--0.1541 Å2
L0.1377 °20.0485 °2-0.1146 °2-1.7336 °20.1375 °2--0.2941 °2
S0.0352 Å °0.0201 Å °0.0317 Å °-0.201 Å °-0.0951 Å °-0.291 Å °0.0408 Å °0.0348 Å °0.024 Å °
Refinement TLS groupSelection details: all

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