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- PDB-1ztx: West Nile Virus Envelope Protein DIII in complex with neutralizin... -

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Basic information

Entry
Database: PDB / ID: 1ztx
TitleWest Nile Virus Envelope Protein DIII in complex with neutralizing E16 antibody Fab
Components
  • Envelope protein
  • Heavy Chain of E16 Antibody
  • Light Chain of E16 Antibody
KeywordsViral protein/Immune system / Antibody / Fab / neutralizing / Virus / Envelope / Viral protein-Immune system COMPLEX
Function / homology
Function and homology information


membrane => GO:0016020 / host cell endoplasmic reticulum membrane / protein dimerization activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane
Similarity search - Function
Immunoglobulin-like - #350 / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Immunoglobulins ...Immunoglobulin-like - #350 / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesWest Nile virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNybakken, G.E. / Oliphant, T. / Diamond, M.S. / Fremont, D.H.
CitationJournal: Nature / Year: 2005
Title: Structural basis of West Nile virus neutralization by a therapeutic antibody.
Authors: Nybakken, G.E. / Oliphant, T. / Johnson, S. / Burke, S. / Diamond, M.S. / Fremont, D.H.
History
DepositionMay 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999SEQUENCE The sequences of the chains H and L were not deposited into any sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Envelope protein
H: Heavy Chain of E16 Antibody
L: Light Chain of E16 Antibody


Theoretical massNumber of molelcules
Total (without water)58,1413
Polymers58,1413
Non-polymers00
Water4,612256
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.400, 83.300, 110.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Envelope protein


Mass: 11391.870 Da / Num. of mol.: 1 / Fragment: Domain III (residues 463-568)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) West Nile virus / Genus: Flavivirus / Production host: Escherichia coli (E. coli) / References: UniProt: Q91KZ4
#2: Antibody Heavy Chain of E16 Antibody


Mass: 23358.928 Da / Num. of mol.: 1 / Fragment: VH and CH1 Domains / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody Light Chain of E16 Antibody


Mass: 23389.871 Da / Num. of mol.: 1 / Fragment: VL and CL Domains / Source method: isolated from a natural source
Details: The Heavy chain and light chain were made from a mouse hybridoma
Source: (natural) Mus musculus (house mouse)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.13 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, Glycine, Hepes, pH 8.5, 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: 1.55 Å
DetectorType: BRUKER PROTEUM / Detector: CCD / Date: Aug 5, 2004
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.55 Å / Relative weight: 1
ReflectionResolution: 2.5→47.32 Å / Num. all: 16985 / Num. obs: 16985 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Redundancy: 3.53 % / Rmerge(I) obs: 0.083 / Χ2: 0.97 / Net I/σ(I): 11.3 / Scaling rejects: 453
Reflection shellResolution: 2.5→2.59 Å / % possible obs: 82.7 % / Redundancy: 1.99 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 2.7 / Num. measured obs: 453 / Χ2: 0.99 / % possible all: 82.7

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation4 Å47.35 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.2LDzdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT1.601data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1S6N, 2IGF

1s6n

2igf


Resolution: 2.5→50 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 817 4.9 %Random
Rwork0.208 ---
all0.221 16985 --
obs0.226 16752 96.4 %-
Solvent computationBsol: 45.345 Å2
Displacement parametersBiso mean: 32.661 Å2
Baniso -1Baniso -2Baniso -3
1--5.236 Å20 Å20 Å2
2--2.312 Å20 Å2
3---2.924 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4040 0 0 256 4296
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d27.4
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.041
RfactorNum. reflection% reflection
Rfree0.318 60 -
Rwork0.256 --
obs-1330 78 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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