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- PDB-30cp: Structure of the Hepatitis C Virus E2 Core from Genotype 6a in Co... -

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Basic information

Entry
Database: PDB / ID: 30cp
TitleStructure of the Hepatitis C Virus E2 Core from Genotype 6a in Complex with Germline Reverted Variants of the Broadly Neutralizing Antibody AR3C
Components
  • Fab AR3C GL heavy chain
  • Fab AR3C GL light chain
  • HCV E2 envelope protein
KeywordsVIRAL PROTEIN / Hepatitis C virus / E2 envelope protein / neutralizing antibodies / Germ line
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
Recombinant Hepatitis C virus HK6a/JFH-1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsYechezkel, I. / Tzarum, N.
Funding support United States, Israel, 2items
OrganizationGrant numberCountry
United States - Israel Binational Science Foundation (BSF)2021-165 United States
Israel Science Foundation1600/21 Israel
CitationJournal: To Be Published
Title: Structural and biochemical studies of the hepatitis C virus envelope proteins to promote germline-targeting vaccine design
Authors: Yechezkel, I. / Maymon, H. / Tennenhouse, A. / Chen, F. / Tarabih, H. / Weisz, J. / Fraenkel, R. / Fleishman, S.J. / law, M. / Tzarum, N.
History
DepositionApr 21, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab AR3C GL heavy chain
L: Fab AR3C GL light chain
D0A0: HCV E2 envelope protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,47116
Polymers70,5433
Non-polymers1,92813
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint17 kcal/mol
Surface area27230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.334, 64.450, 183.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules D0A0

#3: Protein HCV E2 envelope protein


Mass: 20707.395 Da / Num. of mol.: 1 / Mutation: N448D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Recombinant Hepatitis C virus HK6a/JFH-1
Production host: Homo sapiens (human)

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Antibody , 2 types, 2 molecules HL

#1: Antibody Fab AR3C GL heavy chain


Mass: 24364.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Fab AR3C GL light chain


Mass: 25471.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 2 types, 3 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 324 molecules

#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.53 Å3/Da / Density % sol: 51.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES (pH 7.5), 20% (w/v) PEG 4000, and 10% (v/v) isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS4 X 4M / Detector: PIXEL / Date: Jan 29, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.93→44.05 Å / Num. obs: 54095 / % possible obs: 94.8 % / Redundancy: 4.4 % / Biso Wilson estimate: 31.97 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7
Reflection shellResolution: 1.93→2 Å / Num. unique obs: 5240 / CC1/2: 0.32

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Processing

Software
NameVersionClassification
PHASER1.17.1_3660phasing
PHENIX1.17.1_3660refinement
EDNAdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→44.05 Å / SU ML: 0.255 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.9279
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2455 2809 5.23 %
Rwork0.2018 50922 -
obs0.204 53731 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.04 Å2
Refinement stepCycle: LAST / Resolution: 1.93→44.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4593 0 126 314 5033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00884904
X-RAY DIFFRACTIONf_angle_d1.09736663
X-RAY DIFFRACTIONf_chiral_restr0.0666749
X-RAY DIFFRACTIONf_plane_restr0.0069846
X-RAY DIFFRACTIONf_dihedral_angle_d16.0781763
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.960.32551140.30712320X-RAY DIFFRACTION89.88
1.96-20.32991270.29182458X-RAY DIFFRACTION96.53
2-2.040.33311560.27112506X-RAY DIFFRACTION98.81
2.04-2.080.28321580.26682524X-RAY DIFFRACTION99
2.08-2.120.25721420.23772485X-RAY DIFFRACTION98.91
2.12-2.170.30751590.23382542X-RAY DIFFRACTION99.05
2.17-2.230.22391460.23342538X-RAY DIFFRACTION99.33
2.23-2.290.29671220.22382573X-RAY DIFFRACTION99.37
2.29-2.360.30671240.22472556X-RAY DIFFRACTION99.41
2.36-2.430.31721460.21882549X-RAY DIFFRACTION99.45
2.43-2.520.28061380.21182573X-RAY DIFFRACTION99.41
2.52-2.620.27141330.20752565X-RAY DIFFRACTION99.48
2.62-2.740.24811340.19822583X-RAY DIFFRACTION99.34
2.74-2.880.26381280.19362570X-RAY DIFFRACTION99.3
2.88-3.060.20611510.18412466X-RAY DIFFRACTION95.09
3.06-3.30.21281460.18382524X-RAY DIFFRACTION97.8
3.3-3.630.211560.17362604X-RAY DIFFRACTION99.67
3.63-4.160.23141340.17382632X-RAY DIFFRACTION99.53
4.16-5.240.21191580.16312635X-RAY DIFFRACTION98.97
5.24-44.050.25851370.2382719X-RAY DIFFRACTION96.42

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