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- PDB-4oii: West Nile Virus NS1 in complex with neutralizing 22NS1 antibody Fab -

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Basic information

Entry
Database: PDB / ID: 4oii
TitleWest Nile Virus NS1 in complex with neutralizing 22NS1 antibody Fab
Components
  • Heavy Chain of Fab fragment of 22NS1 Antibody
  • Light Chain of Fab fragment of 22NS1 Antibody
  • NON-STRUCTURAL PROTEIN NS1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / West Nile Virus / ANTIBODY / FAB / NEUTRALIZING / FLAVIVIRUS / NON-STRUCTURAL PROTEIN / NS1 / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / induction by virus of host autophagy / virus-mediated perturbation of host defense response / 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 / 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
: / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus non-structural protein NS2B / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A ...: / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus envelope glycoprotein E, stem/anchor domain / 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. / 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 / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesWest Nile virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsEdeling, M.A. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis of Flavivirus NS1 assembly and antibody recognition.
Authors: Edeling, M.A. / Diamond, M.S. / Fremont, D.H.
History
DepositionJan 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Apr 23, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NON-STRUCTURAL PROTEIN NS1
B: NON-STRUCTURAL PROTEIN NS1
L: Light Chain of Fab fragment of 22NS1 Antibody
H: Heavy Chain of Fab fragment of 22NS1 Antibody
M: Light Chain of Fab fragment of 22NS1 Antibody
I: Heavy Chain of Fab fragment of 22NS1 Antibody


Theoretical massNumber of molelcules
Total (without water)135,4736
Polymers135,4736
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14270 Å2
ΔGint-64 kcal/mol
Surface area48590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)215.869, 49.546, 130.075
Angle α, β, γ (deg.)90.00, 91.21, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-304-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN L AND (RESSEQ 1:213 )
211CHAIN M AND (RESSEQ 1:213 )
112CHAIN H AND (RESSEQ 1:53 OR RESSEQ 153:185 OR RESSEQ...
212CHAIN I AND (RESSEQ 1:53 OR RESSEQ 153:185 OR RESSEQ...
113CHAIN A AND (RESSEQ 176:352 )
213CHAIN B AND (RESSEQ 176:352 )

NCS ensembles :
ID
1
2
3

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Components

#1: Protein NON-STRUCTURAL PROTEIN NS1


Mass: 20872.318 Da / Num. of mol.: 2 / Fragment: UNP residues 963-1143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) West Nile virus / Plasmid: pet21(a)+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: U3N977, UniProt: Q9Q6P4*PLUS
#2: Antibody Light Chain of Fab fragment of 22NS1 Antibody


Mass: 23536.924 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Antibody Heavy Chain of Fab fragment of 22NS1 Antibody


Mass: 23327.080 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.57 Å3/Da / Density % sol: 52.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 9 mg/mL in 8% PEG 8K, 0.1 M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Aug 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 28187 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 6.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3-3.113.80.6981100
3.11-3.233.80.5251100
3.23-3.383.80.3751100
3.38-3.563.80.2711100
3.56-3.783.80.1981100
3.78-4.073.80.151100
4.07-4.483.80.091100
4.48-5.133.80.0661100
5.13-6.463.70.0721100
6.46-503.60.0571100

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.14data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→49.467 Å / SU ML: 0.87 / σ(F): 1.45 / Phase error: 26.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2652 1428 5.07 %
Rwork0.2137 --
obs0.2163 28182 99.88 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.485 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.8234 Å2-0 Å211.1203 Å2
2---1.3908 Å2-0 Å2
3---9.2142 Å2
Refinement stepCycle: LAST / Resolution: 3→49.467 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9388 0 0 67 9455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039640
X-RAY DIFFRACTIONf_angle_d0.68213116
X-RAY DIFFRACTIONf_dihedral_angle_d10.6763450
X-RAY DIFFRACTIONf_chiral_restr0.0451458
X-RAY DIFFRACTIONf_plane_restr0.0031678
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11L1655X-RAY DIFFRACTIONPOSITIONAL
12M1655X-RAY DIFFRACTIONPOSITIONAL0.004
21H1517X-RAY DIFFRACTIONPOSITIONAL
22I1517X-RAY DIFFRACTIONPOSITIONAL0.003
31A1398X-RAY DIFFRACTIONPOSITIONAL
32B1398X-RAY DIFFRACTIONPOSITIONAL0.005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.10680.35131410.27932636X-RAY DIFFRACTION99
3.1068-3.23120.34941370.25332607X-RAY DIFFRACTION100
3.2312-3.37820.2961460.23692665X-RAY DIFFRACTION100
3.3782-3.55630.29351380.23232664X-RAY DIFFRACTION100
3.5563-3.7790.27271470.2092649X-RAY DIFFRACTION100
3.779-4.07070.23181360.19642676X-RAY DIFFRACTION100
4.0707-4.48010.21741450.17382671X-RAY DIFFRACTION100
4.4801-5.12780.20361390.17232661X-RAY DIFFRACTION100
5.1278-6.45820.25521450.21172715X-RAY DIFFRACTION100
6.4582-49.47350.30521540.24322810X-RAY DIFFRACTION100

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