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- PDB-4ffy: Crystal structure of DENV1-E111 single chain variable fragment bo... -

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Basic information

Entry
Database: PDB / ID: 4ffy
TitleCrystal structure of DENV1-E111 single chain variable fragment bound to DENV-1 DIII, strain 16007.
Components
  • (DENV1-E111 single chain variable fragment ...) x 2
  • envelope glycoprotein
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / Viral envelope proteins / structural genomics / antibody epitopes / Flavivirus / Dengue virus / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / 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 / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Immunoglobulin-like - #350 / : / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus non-structural protein NS2B / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus ...Immunoglobulin-like - #350 / : / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus non-structural protein NS2B / Flavivirus envelope glycoprotein E, stem/anchor domain / : / 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. / 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, flavivirus / Flavivirus envelope glycoprotein M / 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 / Immunoglobulins / 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 speciesMus musculus (house mouse)
Dengue virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsAustin, S.K. / Nelson, C.A. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Plos Pathog. / Year: 2012
Title: Structural Basis of Differential Neutralization of DENV-1 Genotypes by an Antibody that Recognizes a Cryptic Epitope.
Authors: Austin, S.K. / Dowd, K.A. / Shrestha, B. / Nelson, C.A. / Edeling, M.A. / Johnson, S. / Pierson, T.C. / Diamond, M.S. / Fremont, D.H.
History
DepositionJun 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: DENV1-E111 single chain variable fragment (light chain)
H: DENV1-E111 single chain variable fragment (heavy chain)
A: envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2309
Polymers39,9003
Non-polymers3306
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-19 kcal/mol
Surface area14430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.330, 135.330, 52.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#3: Protein envelope glycoprotein


Mass: 11985.743 Da / Num. of mol.: 1 / Fragment: UNP residues 573-679
Source method: isolated from a genetically manipulated source
Details: refolded / Source: (gene. exp.) Dengue virus 1 / Strain: 16007 / Gene: Envelope domain III / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9J7C6

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Antibody , 2 types, 2 molecules LH

#1: Antibody DENV1-E111 single chain variable fragment (light chain)


Mass: 13046.097 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: soluble / Source: (gene. exp.) Mus musculus (house mouse) / Strain: IFN-aBR-/- C57BL/6 mice / Plasmid: pAK400 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL
#2: Antibody DENV1-E111 single chain variable fragment (heavy chain)


Mass: 14868.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: soluble / Source: (gene. exp.) Mus musculus (house mouse) / Strain: IFN-aBR-/- C57BL/6 mice / Plasmid: pAK400 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL

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Non-polymers , 4 types, 144 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 3 Å3/Da / Density % sol: 58.97 %
Crystal growTemperature: 293 K / pH: 7.4
Details: 20% PEG 3350, 0.2M Potassium sulfate, and 5% glycerol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.007
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 17132 / % possible obs: 98.1 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 18.78
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.35 / % possible all: 94.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.72 Å28.51 Å
Translation2.72 Å28.51 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→41.35 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.41 / σ(F): 1.34 / Phase error: 22.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 853 4.99 %
Rwork0.174 --
obs0.176 17091 98.1 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.36 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 54.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.8509 Å20 Å2-0 Å2
2--0.8509 Å20 Å2
3----1.7017 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2562 0 15 138 2715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042639
X-RAY DIFFRACTIONf_angle_d0.8833580
X-RAY DIFFRACTIONf_dihedral_angle_d12.746944
X-RAY DIFFRACTIONf_chiral_restr0.06386
X-RAY DIFFRACTIONf_plane_restr0.003457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4964-2.65280.46081390.3312547X-RAY DIFFRACTION95
2.6528-2.85760.28931290.2392568X-RAY DIFFRACTION95
2.8576-3.1450.25221420.18582702X-RAY DIFFRACTION99
3.145-3.59990.24911440.17182726X-RAY DIFFRACTION100
3.5999-4.53460.19831470.14152787X-RAY DIFFRACTION100
4.5346-41.36110.19591520.16352908X-RAY DIFFRACTION100

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