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- PDB-4kvc: 2H2 Fab fragment of immature Dengue virus -

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Basic information

Entry
Database: PDB / ID: 4kvc
Title2H2 Fab fragment of immature Dengue virus
Components
  • Ig heavy chain V region MOPC 21, Igh protein
  • Ig kappa chain V-V region MOPC 21, Anti-colorectal carcinoma light chain
KeywordsIMMUNE SYSTEM / Fab fragment / immature Dengue / pr peptide
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / immune response / extracellular space
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig kappa chain V-V region MOPC 21 / : / Igh protein / Anti-colorectal carcinoma light chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.306 Å
AuthorsWang, Z. / Rossmann, M.G.
CitationJournal: J Virol / Year: 2013
Title: Obstruction of dengue virus maturation by Fab fragments of the 2H2 antibody.
Authors: Zhiqing Wang / Long Li / Janice G Pennington / Ju Sheng / Moh Lan Yap / Pavel Plevka / Geng Meng / Lei Sun / Wen Jiang / Michael G Rossmann /
Abstract: The 2H2 monoclonal antibody recognizes the precursor peptide on immature dengue virus and might therefore be a useful tool for investigating the conformational change that occurs when the immature ...The 2H2 monoclonal antibody recognizes the precursor peptide on immature dengue virus and might therefore be a useful tool for investigating the conformational change that occurs when the immature virus enters an acidic environment. During dengue virus maturation, spiky, immature, noninfectious virions change their structure to form smooth-surfaced particles in the slightly acidic environment of the trans-Golgi network, thereby allowing cellular furin to cleave the precursor-membrane proteins. The dengue virions become fully infectious when they release the cleaved precursor peptide upon reaching the neutral-pH environment of the extracellular space. Here we report on the cryo-electron microscopy structures of the immature virus complexed with the 2H2 antigen binding fragments (Fab) at different concentrations and under various pH conditions. At neutral pH and a high concentration of Fab molecules, three Fab molecules bind to three precursor-membrane proteins on each spike of the immature virus. However, at a low concentration of Fab molecules and pH 7.0, only two Fab molecules bind to each spike. Changing to a slightly acidic pH caused no detectable change of structure for the sample with a high Fab concentration but caused severe structural damage to the low-concentration sample. Therefore, the 2H2 Fab inhibits the maturation process of immature dengue virus when Fab molecules are present at a high concentration, because the three Fab molecules on each spike hold the precursor-membrane molecules together, thereby inhibiting the normal conformational change that occurs during maturation.
History
DepositionMay 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Ig heavy chain V region MOPC 21, Igh protein
L: Ig kappa chain V-V region MOPC 21, Anti-colorectal carcinoma light chain


Theoretical massNumber of molelcules
Total (without water)47,0712
Polymers47,0712
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-23 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.554, 81.711, 85.306
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Antibody Ig heavy chain V region MOPC 21, Igh protein


Mass: 23641.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell: hybridoma / Gene: Igh-1a, Igh / Production host: Mus musculus (house mouse) / References: UniProt: P01783, UniProt: Q6PIP8
#2: Antibody Ig kappa chain V-V region MOPC 21, Anti-colorectal carcinoma light chain


Mass: 23429.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell: hybridoma / Gene: Gm16939 / Production host: Mus musculus (house mouse) / References: UniProt: P01634, UniProt: Q7TS98
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 1.93 Å3/Da / Density % sol: 36.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% PEG 6000 0.1 M MES 0.2M NH4Cl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 31, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 16461 / Num. obs: 16461 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 24.7
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
2.3-2.340.4111100
2.34-2.380.3791100
2.38-2.430.3551100
2.43-2.480.2981100
2.48-2.530.2791100
2.53-2.590.2461100

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.306→44 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 832 5.07 %Random
Rwork0.179 ---
all0.1818 16483 --
obs0.1818 16417 --
Displacement parametersBiso mean: 23.6237 Å2
Refinement stepCycle: LAST / Resolution: 2.306→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3305 0 0 156 3461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083389
X-RAY DIFFRACTIONf_angle_d1.24610
X-RAY DIFFRACTIONf_chiral_restr0.079518
X-RAY DIFFRACTIONf_plane_restr0.005586
X-RAY DIFFRACTIONf_dihedral_angle_d15.931200

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