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- PDB-3i50: Crystal structure of the West Nile Virus envelope glycoprotein in... -

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Basic information

Entry
Database: PDB / ID: 3i50
TitleCrystal structure of the West Nile Virus envelope glycoprotein in complex with the E53 antibody Fab
Components
  • Envelope glycoprotein
  • murine heavy chain (IgG3) of E53 monoclonal antibody Fab
  • murine kappa light chain of E53 monoclonal antibody Fab
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / ANTIBODY / FAB / VIRUS / ENVELOPE / IMMUNOGLOBULIN / FUSION LOOP / Disulfide bond / Envelope protein / Membrane / Transmembrane / Virion / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-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 / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A ...Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / 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, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / 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 / DNA/RNA polymerase superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein / Genome polyprotein
Similarity search - Component
Biological speciesWest Nile virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsNybakken, G.E. / Warren, J.T. / Chen, B.R. / Nelson, C.A. / Fremont, D.H.
CitationJournal: EMBO J / Year: 2009
Title: Structural basis for the preferential recognition of immature flaviviruses by a fusion-loop antibody.
Authors: Mickaël V Cherrier / Bärbel Kaufmann / Grant E Nybakken / Shee-Mei Lok / Julia T Warren / Beverly R Chen / Christopher A Nelson / Victor A Kostyuchenko / Heather A Holdaway / Paul R ...Authors: Mickaël V Cherrier / Bärbel Kaufmann / Grant E Nybakken / Shee-Mei Lok / Julia T Warren / Beverly R Chen / Christopher A Nelson / Victor A Kostyuchenko / Heather A Holdaway / Paul R Chipman / Richard J Kuhn / Michael S Diamond / Michael G Rossmann / Daved H Fremont /
Abstract: Flaviviruses are a group of human pathogens causing severe encephalitic or hemorrhagic diseases that include West Nile, dengue and yellow fever viruses. Here, using X-ray crystallography we have ...Flaviviruses are a group of human pathogens causing severe encephalitic or hemorrhagic diseases that include West Nile, dengue and yellow fever viruses. Here, using X-ray crystallography we have defined the structure of the flavivirus cross-reactive antibody E53 that engages the highly conserved fusion loop of the West Nile virus envelope glycoprotein. Using cryo-electron microscopy, we also determined that E53 Fab binds preferentially to spikes in noninfectious, immature flavivirions but is unable to bind significantly to mature virions, consistent with the limited solvent exposure of the epitope. We conclude that the neutralizing impact of E53 and likely similar fusion-loop-specific antibodies depends on its binding to the frequently observed immature component of flavivirus particles. Our results elucidate how fusion-loop antibodies, which comprise a significant fraction of the humoral response against flaviviruses, can function to control infection without appreciably recognizing mature virions. As these highly cross-reactive antibodies are often weakly neutralizing they also may contribute to antibody-dependent enhancement and flavi virus pathogenesis thereby complicating development of safe and effective vaccines.
History
DepositionJul 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 25, 2013Group: Derived calculations
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Envelope glycoprotein
L: murine kappa light chain of E53 monoclonal antibody Fab
H: murine heavy chain (IgG3) of E53 monoclonal antibody Fab


Theoretical massNumber of molelcules
Total (without water)89,6593
Polymers89,6593
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-33 kcal/mol
Surface area33310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.41, 160.14, 43.88
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Envelope glycoprotein


Mass: 43416.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) West Nile virus / Strain: NY 1999 / Gene: ENVELOPE / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q91R02, UniProt: Q9Q6P4*PLUS
#2: Antibody murine kappa light chain of E53 monoclonal antibody Fab


Mass: 22577.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/c / Description: B-cell hybridoma cells / Cell: hybridoma / Gene: Light chain of E53 antibody / Production host: Mus musculus (house mouse)
#3: Antibody murine heavy chain (IgG3) of E53 monoclonal antibody Fab


Mass: 23665.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/c / Description: B-cell hybridoma cells / Cell: hybridoma / Gene: Heavy chain of E53 antibody / Production host: Mus musculus (house mouse)
Has protein modificationY

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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: 2.87 Å3/Da / Density % sol: 57.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 300, 0.1 M MES, pH 6.5, 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: 1.24 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jun 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 3→50.15 Å / Num. all: 21544 / Num. obs: 21428 / % possible obs: 99.5 % / Redundancy: 4.45 % / Biso Wilson estimate: 110.6 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 12.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 4.39 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2 / Num. unique all: 2119 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
d*TREK9.4Ddata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ALS4.2.2data collection
d*TREKdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→20 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.98 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.344 1026 5.11 %random
Rwork0.247 ---
obs-20060 93.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 91.349 Å2 / ksol: 0.307 e/Å3
Displacement parametersBiso max: 321.43 Å2 / Biso mean: 146.439 Å2 / Biso min: 42.65 Å2
Baniso -1Baniso -2Baniso -3
1--21.327 Å2-0 Å20 Å2
2---48.139 Å2-0 Å2
3---69.465 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5283 0 0 0 5283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045412
X-RAY DIFFRACTIONf_angle_d0.8587344
X-RAY DIFFRACTIONf_chiral_restr0.056834
X-RAY DIFFRACTIONf_plane_restr0.003926
X-RAY DIFFRACTIONf_dihedral_angle_d17.2221892
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
3-3.1580.41350.33423992534253484
3.158-3.3550.3861160.28825752691269189
3.355-3.6120.3951230.26426502773277393
3.612-3.9730.3751560.24927002856285694
3.973-4.5420.2831570.20428002957295798
4.542-5.70.2991720.21528823054305498
5.7-19.8580.3691670.25930283195319599
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.79441.5795-0.18571.23550.18461.379-0.09210.05070.85010.2253-0.00360.59950.24450.08430.05341.03250.02270.29880.92880.23211.2649-46.039936.9635-0.4221
21.2661-0.0294-0.15221.2075-0.83390.3852-0.036-0.0671-0.2637-0.32630.07470.2840.33540.2872-0.02550.6554-0.05170.05730.65540.09340.5607-14.070355.8659-33.0326
31.5336-0.9357-0.91733.6035-1.54982.6666-0.11640.25840.1412-0.1119-0.2511-0.73790.1331-0.65520.2980.4644-0.0087-0.06220.44120.09710.28826.334587.0991-52.5027
40.4362-2.3935-0.00352.0054-3.53760.3548-0.7271-0.03681.15450.2386-0.3141-1.92580.1235-0.00010.9221.48880.0746-0.79290.8174-0.03492.490358.404795.8044-38.3054
50.6361.51872.10236.06271.37683.86980.4137-0.062-0.43210.3702-0.0813-1.46720.0826-0.3498-0.26040.39550.0193-0.24550.40360.02560.627329.730866.8675-43.8165
63.79770.4765-1.9769-1.87951.0473.6853-0.6818-0.1967-1.84212.3494-0.561-1.90430.90130.22790.88862.02550.162-0.95760.67190.23152.175150.819783.8884-27.4749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain E and (resid 7:51 or resid 134:195 or resid 284:297))E7 - 51
2X-RAY DIFFRACTION1(chain E and (resid 7:51 or resid 134:195 or resid 284:297))E134 - 195
3X-RAY DIFFRACTION1(chain E and (resid 7:51 or resid 134:195 or resid 284:297))E284 - 297
4X-RAY DIFFRACTION2(chain E and (resid 52:133 or resid 196:283))E52 - 133
5X-RAY DIFFRACTION2(chain E and (resid 52:133 or resid 196:283))E196 - 283
6X-RAY DIFFRACTION3(chain L and resid 1:107)L1 - 107
7X-RAY DIFFRACTION4(chain L and resid 108:208)L108 - 208
8X-RAY DIFFRACTION5(chain H and resid 1:111)H1 - 111
9X-RAY DIFFRACTION6(chain H and resid 112:211)H112 - 211

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