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

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Basic information

Entry
Database: PDB / ID: 4wht
TitleStructure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423 bound to the broadly neutralizing antibody 3/11, P1 crystal form
Components
  • Epitope peptide
  • Heavy chain of the Fab fragment derived from neutralizing antibody 3/11
  • Light chain of the Fab fragment derived from neutralizing antibody 3/11
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 / molecular replacement / Resolution: 2.22 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 23, 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: Heavy chain of the Fab fragment derived from neutralizing antibody 3/11
C: Heavy chain of the Fab fragment derived from neutralizing antibody 3/11
E: Heavy chain of the Fab fragment derived from neutralizing antibody 3/11
G: Heavy chain of the Fab fragment derived from neutralizing antibody 3/11
I: Heavy chain of the Fab fragment derived from neutralizing antibody 3/11
J: Light chain of the Fab fragment derived from neutralizing antibody 3/11
K: Heavy chain of the Fab fragment derived from neutralizing antibody 3/11
M: Heavy chain of the Fab fragment derived from neutralizing antibody 3/11
O: Heavy chain of the Fab fragment derived from neutralizing antibody 3/11
Q: Heavy chain of the Fab fragment derived from neutralizing antibody 3/11
S: Heavy chain of the Fab fragment derived from neutralizing antibody 3/11
U: Heavy chain of the Fab fragment derived from neutralizing antibody 3/11
X: Heavy chain of the Fab fragment derived from neutralizing antibody 3/11
B: Light chain of the Fab fragment derived from neutralizing antibody 3/11
D: Light chain of the Fab fragment derived from neutralizing antibody 3/11
F: Light chain of the Fab fragment derived from neutralizing antibody 3/11
H: Light chain of the Fab fragment derived from neutralizing antibody 3/11
L: Light chain of the Fab fragment derived from neutralizing antibody 3/11
N: Light chain of the Fab fragment derived from neutralizing antibody 3/11
P: Light chain of the Fab fragment derived from neutralizing antibody 3/11
R: Light chain of the Fab fragment derived from neutralizing antibody 3/11
T: Light chain of the Fab fragment derived from neutralizing antibody 3/11
V: Light chain of the Fab fragment derived from neutralizing antibody 3/11
Y: Light chain of the Fab fragment derived from neutralizing antibody 3/11
a: Epitope peptide
c: Epitope peptide
e: Epitope peptide
g: Epitope peptide
i: Epitope peptide
k: Epitope peptide
m: Epitope peptide
o: Epitope peptide
q: Epitope peptide
s: Epitope peptide
u: Epitope peptide
x: Epitope peptide


Theoretical massNumber of molelcules
Total (without water)626,24236
Polymers626,24236
Non-polymers00
Water15,313850
1
A: Heavy chain of the Fab fragment derived from neutralizing antibody 3/11
B: Light chain of the Fab fragment derived from neutralizing antibody 3/11
a: Epitope peptide


Theoretical massNumber of molelcules
Total (without water)52,1873
Polymers52,1873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-32 kcal/mol
Surface area19480 Å2
MethodPISA
2
C: Heavy chain of the Fab fragment derived from neutralizing antibody 3/11
D: Light chain of the Fab fragment derived from neutralizing antibody 3/11
c: Epitope peptide


Theoretical massNumber of molelcules
Total (without water)52,1873
Polymers52,1873
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-30 kcal/mol
Surface area19240 Å2
MethodPISA
3
E: Heavy chain of the Fab fragment derived from neutralizing antibody 3/11
F: Light chain of the Fab fragment derived from neutralizing antibody 3/11
e: Epitope peptide


Theoretical massNumber of molelcules
Total (without water)52,1873
Polymers52,1873
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-32 kcal/mol
Surface area19200 Å2
MethodPISA
4
G: Heavy chain of the Fab fragment derived from neutralizing antibody 3/11
H: Light chain of the Fab fragment derived from neutralizing antibody 3/11
g: Epitope peptide


Theoretical massNumber of molelcules
Total (without water)52,1873
Polymers52,1873
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-32 kcal/mol
Surface area19500 Å2
MethodPISA
5
I: Heavy chain of the Fab fragment derived from neutralizing antibody 3/11
J: Light chain of the Fab fragment derived from neutralizing antibody 3/11
i: Epitope peptide


Theoretical massNumber of molelcules
Total (without water)52,1873
Polymers52,1873
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-31 kcal/mol
Surface area19340 Å2
MethodPISA
6
K: Heavy chain of the Fab fragment derived from neutralizing antibody 3/11
L: Light chain of the Fab fragment derived from neutralizing antibody 3/11
k: Epitope peptide


Theoretical massNumber of molelcules
Total (without water)52,1873
Polymers52,1873
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-30 kcal/mol
Surface area19170 Å2
MethodPISA
7
M: Heavy chain of the Fab fragment derived from neutralizing antibody 3/11
N: Light chain of the Fab fragment derived from neutralizing antibody 3/11
m: Epitope peptide


Theoretical massNumber of molelcules
Total (without water)52,1873
Polymers52,1873
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-31 kcal/mol
Surface area19320 Å2
MethodPISA
8
O: Heavy chain of the Fab fragment derived from neutralizing antibody 3/11
P: Light chain of the Fab fragment derived from neutralizing antibody 3/11
o: Epitope peptide


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-32 kcal/mol
Surface area19360 Å2
MethodPISA
9
Q: Heavy chain of the Fab fragment derived from neutralizing antibody 3/11
R: Light chain of the Fab fragment derived from neutralizing antibody 3/11
q: Epitope peptide


Theoretical massNumber of molelcules
Total (without water)52,1873
Polymers52,1873
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-31 kcal/mol
Surface area19360 Å2
MethodPISA
10
S: Heavy chain of the Fab fragment derived from neutralizing antibody 3/11
T: Light chain of the Fab fragment derived from neutralizing antibody 3/11
s: Epitope peptide


Theoretical massNumber of molelcules
Total (without water)52,1873
Polymers52,1873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-32 kcal/mol
Surface area18940 Å2
MethodPISA
11
U: Heavy chain of the Fab fragment derived from neutralizing antibody 3/11
V: Light chain of the Fab fragment derived from neutralizing antibody 3/11
u: Epitope peptide


Theoretical massNumber of molelcules
Total (without water)52,1873
Polymers52,1873
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-31 kcal/mol
Surface area19190 Å2
MethodPISA
12
X: Heavy chain of the Fab fragment derived from neutralizing antibody 3/11
Y: Light chain of the Fab fragment derived from neutralizing antibody 3/11
x: Epitope peptide


Theoretical massNumber of molelcules
Total (without water)52,1873
Polymers52,1873
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-31 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.794, 128.225, 163.626
Angle α, β, γ (deg.)88.790, 94.360, 96.150
Int Tables number1
Space group name H-MP1
DetailsThe biological unit is a heterotrimer containing heavy and light chain of the Fab fragment and one synthetic peptide. There are 12 biological units in the asymmetric unit (chains A&B+a, chains C&D+c, chains E&F+e, chains G&H+g, chains I&J+i, chains K&L+k, chains M&N+m, chains O&P+o, chains Q&R+q, chains S&T+s, chains U&V+u, chains X&Y+x).

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Components

#1: Antibody
Heavy chain of the Fab fragment derived from neutralizing antibody 3/11


Mass: 26893.855 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pMT/BiP based / Cell line (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly)
#2: Antibody
Light chain of the Fab fragment derived from neutralizing antibody 3/11


Mass: 23909.492 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly)
#3: Protein/peptide
Epitope peptide


Mass: 1383.489 Da / Num. of mol.: 12 / Fragment: UNP residues 51-62
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus / Production host: synthetic construct (others) / References: UniProt: Q9WJJ4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 850 / 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: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM TRIS, 27% PEG4000, 100mM Na-Acetate

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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: Jul 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97902 Å / Relative weight: 1
ReflectionResolution: 2.22→48.74 Å / Num. obs: 246066 / % possible obs: 95.4 % / Redundancy: 2.4 % / Biso Wilson estimate: 39.67 Å2 / Net I/σ(I): 9
Reflection shellResolution: 2.22→2.34 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 1.8 / % possible all: 81.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
PHASERphasing
BUSTER2.11.2refinement
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→32.5 Å / Cor.coef. Fo:Fc: 0.8968 / Cor.coef. Fo:Fc free: 0.8698 / SU R Cruickshank DPI: 0.322 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.298 / SU Rfree Blow DPI: 0.213 / SU Rfree Cruickshank DPI: 0.221
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 12380 5.03 %RANDOM
Rwork0.2091 ---
obs0.2108 246026 95.39 %-
Displacement parametersBiso max: 141.01 Å2 / Biso mean: 41.72 Å2 / Biso min: 8.07 Å2
Baniso -1Baniso -2Baniso -3
1-6.844 Å21.0365 Å2-2.4396 Å2
2---3.5846 Å2-13.755 Å2
3----3.2594 Å2
Refine analyzeLuzzati coordinate error obs: 0.325 Å
Refinement stepCycle: final / Resolution: 2.22→32.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39249 0 0 850 40099
Biso mean---34.87 -
Num. residues----5168
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d13251SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes798HARMONIC2
X-RAY DIFFRACTIONt_gen_planes5847HARMONIC5
X-RAY DIFFRACTIONt_it40136HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion5501SEMIHARMONIC5
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_contact43552SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d40136HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg54718HARMONIC21.23
X-RAY DIFFRACTIONt_omega_torsion3.34
X-RAY DIFFRACTIONt_other_torsion19.12
LS refinement shellResolution: 2.22→2.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2566 733 4.96 %
Rwork0.2332 14051 -
all0.2343 14784 -
obs--95.39 %

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