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- PDB-6wy1: Crystal structure of an engineered thermostable dengue virus 2 en... -

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Basic information

Entry
Database: PDB / ID: 6wy1
TitleCrystal structure of an engineered thermostable dengue virus 2 envelope protein dimer
ComponentsDengue 2 soluble recombinant envelope
KeywordsVIRAL PROTEIN / Dengue virus / envelope protein / thermostable / computational protein design / protein engineering
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 ...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 / induction by virus of host autophagy / 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 / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / 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 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesDengue virus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.42 Å
AuthorsKudlacek, S.T. / Lakshmanane, P. / Kuhlman, B.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W81XWH1820035 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5 F31 AI145408-02 United States
CitationJournal: Sci Adv / Year: 2021
Title: Designed, highly expressing, thermostable dengue virus 2 envelope protein dimers elicit quaternary epitope antibodies.
Authors: Kudlacek, S.T. / Metz, S. / Thiono, D. / Payne, A.M. / Phan, T.T.N. / Tian, S. / Forsberg, L.J. / Maguire, J. / Seim, I. / Zhang, S. / Tripathy, A. / Harrison, J. / Nicely, N.I. / Soman, S. ...Authors: Kudlacek, S.T. / Metz, S. / Thiono, D. / Payne, A.M. / Phan, T.T.N. / Tian, S. / Forsberg, L.J. / Maguire, J. / Seim, I. / Zhang, S. / Tripathy, A. / Harrison, J. / Nicely, N.I. / Soman, S. / McCracken, M.K. / Gromowski, G.D. / Jarman, R.G. / Premkumar, L. / de Silva, A.M. / Kuhlman, B.
History
DepositionMay 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dengue 2 soluble recombinant envelope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9162
Polymers45,6941
Non-polymers2211
Water0
1
A: Dengue 2 soluble recombinant envelope
hetero molecules

A: Dengue 2 soluble recombinant envelope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,8314
Polymers91,3892
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z1
Buried area3950 Å2
ΔGint-10 kcal/mol
Surface area38280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.800, 125.800, 142.637
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z
#3: y,-x+y,z
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z
#9: y,x,-z
#10: -y,-x,-z
#11: -x+y,y,-z
#12: x,x-y,-z

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Components

#1: Protein Dengue 2 soluble recombinant envelope


Mass: 45694.324 Da / Num. of mol.: 1 / Mutation: G106D, A259W, T262R, F279W, T280P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 2 / Plasmid: P-alphaH / Cell line (production host): EXPI293F / Production host: Homo sapiens (human) / References: UniProt: D0EPS0
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN

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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: 3.47 Å3/Da / Density % sol: 64.54 % / Description: Hexagonal plate crystals
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 15% PEG 3350 pH 4.4, 0.1M Sodium Acetate Trihydrate + 0.1M Sodium Iodide
Temp details: 21 degree C

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 19, 2019 / Details: Si 111
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.42→86.58 Å / Num. obs: 9507 / % possible obs: 99.8 % / Redundancy: 16.1 % / Biso Wilson estimate: 92.9 Å2 / CC1/2: 0.982 / Rpim(I) all: 0.162 / Χ2: 1.22 / Net I/σ(I): 9.2
Reflection shellResolution: 3.42→3.69 Å / Redundancy: 16.2 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1901 / CC1/2: 0.693 / Rpim(I) all: 1.264 / % possible all: 99.6

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Processing

Software
NameVersionClassification
XDSMar 15, 2019data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OAN

1oan


Resolution: 3.42→59.67 Å / SU ML: 0.62 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 44.54
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3366 446 4.9 %
Rwork0.3175 8664 -
obs0.3187 9110 95.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.06 Å2
Refinement stepCycle: LAST / Resolution: 3.42→59.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3005 0 14 0 3019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023082
X-RAY DIFFRACTIONf_angle_d0.4814163
X-RAY DIFFRACTIONf_chiral_restr0.042464
X-RAY DIFFRACTIONf_plane_restr0.005531
X-RAY DIFFRACTIONf_dihedral_angle_d14.3891167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.42-3.910.49261130.44912639X-RAY DIFFRACTION89.41
3.92-4.930.34151590.30862887X-RAY DIFFRACTION97.63
4.93-59.670.28921740.2763138X-RAY DIFFRACTION99.43

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