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- PDB-4why: Structure of the Hepatitis C virus envelope glycoprotein E2 antig... -

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Basic information

Entry
Database: PDB / ID: 4why
TitleStructure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423 bound to the broadly neutralizing antibody 3/11, P21 crystal form
Components
  • Heavy chain of Fab fragment derived from neutralizing antibody 3/11
  • Light chain of Fab fragment derived from neutralizing antibody 3/11
  • epitope peptide
KeywordsVIRAL PROTEIN / neutralizing epitope / envelope glycoprotein / E2 / receptor-binding
Function / homology
Function and homology information


host cell lipid droplet / lipid droplet / clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / viral envelope / virion membrane / membrane
Similarity search - Function
Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
Hepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsKrey, T. / Rey, F.A.
Funding support France, 1items
OrganizationGrant numberCountry
ANRS France
CitationJournal: J.Virol. / Year: 2015
Title: Structural flexibility of a conserved antigenic region in hepatitis C virus glycoprotein e2 recognized by broadly neutralizing antibodies.
Authors: Meola, A. / Tarr, A.W. / England, P. / Meredith, L.W. / McClure, C.P. / Foung, S.K. / McKeating, J.A. / Ball, J.K. / Rey, F.A. / Krey, T.
History
DepositionSep 24, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: epitope peptide
B: epitope peptide
C: epitope peptide
D: epitope peptide
G: Heavy chain of Fab fragment derived from neutralizing antibody 3/11
H: Light chain of Fab fragment derived from neutralizing antibody 3/11
I: Heavy chain of Fab fragment derived from neutralizing antibody 3/11
J: Light chain of Fab fragment derived from neutralizing antibody 3/11
K: Heavy chain of Fab fragment derived from neutralizing antibody 3/11
L: Light chain of Fab fragment derived from neutralizing antibody 3/11
M: Heavy chain of Fab fragment derived from neutralizing antibody 3/11
N: Light chain of Fab fragment derived from neutralizing antibody 3/11


Theoretical massNumber of molelcules
Total (without water)208,74712
Polymers208,74712
Non-polymers00
Water2,810156
1
A: epitope peptide
I: Heavy chain of Fab fragment derived from neutralizing antibody 3/11
J: Light chain of Fab fragment derived from neutralizing antibody 3/11


Theoretical massNumber of molelcules
Total (without water)52,1873
Polymers52,1873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-31 kcal/mol
Surface area18930 Å2
MethodPISA
2
B: epitope peptide
M: Heavy chain of Fab fragment derived from neutralizing antibody 3/11
N: Light chain of Fab fragment derived from neutralizing antibody 3/11


Theoretical massNumber of molelcules
Total (without water)52,1873
Polymers52,1873
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-30 kcal/mol
Surface area19030 Å2
MethodPISA
3
C: epitope peptide
K: Heavy chain of Fab fragment derived from neutralizing antibody 3/11
L: Light chain of Fab fragment derived from neutralizing antibody 3/11


Theoretical massNumber of molelcules
Total (without water)52,1873
Polymers52,1873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-32 kcal/mol
Surface area19240 Å2
MethodPISA
4
D: epitope peptide
G: Heavy chain of Fab fragment derived from neutralizing antibody 3/11
H: Light chain of Fab fragment derived from neutralizing antibody 3/11


Theoretical massNumber of molelcules
Total (without water)52,1873
Polymers52,1873
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-31 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.760, 205.510, 69.020
Angle α, β, γ (deg.)90.000, 103.180, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a heterotrimer containing heavy and light chain of the Fab fragment and one synthetic peptide. There are 4 biological units in the asymmetric unit (chains M&N+B, chains G&H+D, chains K&L+C, chains I&J+A).

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Components

#1: Protein/peptide
epitope peptide


Mass: 1383.489 Da / Num. of mol.: 4 / Fragment: UNP residues 51-62 / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Hepatitis C virus / References: UniProt: Q9WJJ4
#2: Antibody
Heavy chain of Fab fragment derived from neutralizing antibody 3/11


Mass: 26893.855 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: IgG / Plasmid: pMT/BiP based / Production host: Drosophila melanogaster (fruit fly)
#3: Antibody
Light chain of Fab fragment derived from neutralizing antibody 3/11


Mass: 23909.492 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: IgG / Plasmid: pMT/BiP based / Production host: Drosophila melanogaster (fruit fly)
#4: 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: 2.14 Å3/Da / Density % sol: 42.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM TRIS, 66% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97902 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97902 Å / Relative weight: 1
ReflectionResolution: 2.62→50 Å / Num. obs: 51028 / % possible obs: 97 % / Redundancy: 3.2 % / Biso Wilson estimate: 64.77 Å2 / Net I/σ(I): 9.9
Reflection shellResolution: 2.62→2.76 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 1.6 / % possible all: 87.5

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.15data extraction
XDSdata reduction
BUSTER2.11.2refinement
XSCALEdata scaling
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→47.97 Å / Cor.coef. Fo:Fc: 0.8688 / Cor.coef. Fo:Fc free: 0.8381 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 3.351 / SU Rfree Blow DPI: 0.334
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2540 5 %RANDOM
Rwork0.2041 ---
obs0.2067 50781 96.6 %-
Displacement parametersBiso max: 143.15 Å2 / Biso mean: 59.56 Å2 / Biso min: 16.47 Å2
Baniso -1Baniso -2Baniso -3
1-6.5084 Å20 Å2-2.9875 Å2
2--22.1664 Å20 Å2
3----28.6748 Å2
Refine analyzeLuzzati coordinate error obs: 0.338 Å
Refinement stepCycle: final / Resolution: 2.62→47.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13022 0 0 156 13178
Biso mean---47.66 -
Num. residues----1709
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4397SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes267HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1932HARMONIC5
X-RAY DIFFRACTIONt_it13313HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1821SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14616SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13313HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg18145HARMONIC21.25
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion20.71
LS refinement shellResolution: 2.62→2.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3073 160 4.96 %
Rwork0.2416 3066 -
all0.2447 3226 -
obs--96.6 %

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