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

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Basic information

Entry
Database: PDB / ID: 30bg
TitleStructure of the Hepatitis C Virus E2 Core from Genotype 6a in Complex with 1-69 Germline-Reverted Variants of the Broadly Neutralizing Antibody U1
Components
  • Fab U1 1-69 heavy chain
  • Fab U1 1-69 light chain
  • HCV E2 envelope protein
KeywordsVIRAL PROTEIN / Hepatitis C virus / E2 envelope protein / neutralizing antibodies / Germ line
Biological speciesRecombinant Hepatitis C virus HK6a/JFH-1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 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 19, 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
E: HCV E2 envelope protein
H: Fab U1 1-69 heavy chain
L: Fab U1 1-69 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7565
Polymers68,3143
Non-polymers4422
Water27015
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-25 kcal/mol
Surface area26870 Å2
Unit cell
Length a, b, c (Å)59.849, 79.072, 133.510
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

#1: Protein HCV E2 envelope protein


Mass: 20707.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Recombinant Hepatitis C virus HK6a/JFH-1
Production host: Homo sapiens (human)
#2: Antibody Fab U1 1-69 heavy chain


Mass: 24269.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Fab U1 1-69 light chain


Mass: 23336.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Potassium chloride, and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS4 X 4M / Detector: PIXEL / Date: May 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 3.3→54.61 Å / Num. obs: 9197 / % possible obs: 92.2 % / Redundancy: 1.7 % / Biso Wilson estimate: 82.01 Å2 / CC1/2: 0.97 / Rmerge(I) obs: 0.683 / Net I/σ(I): 5.1
Reflection shellResolution: 3.3→3.36 Å / Num. unique obs: 480 / CC1/2: 0.33

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Processing

Software
NameVersionClassification
PHASES1.17.1_3660phasing
PHENIX1.17.1_3660refinement
autoPROCdata reduction
autoPROCdata scaling
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.31→54.61 Å / SU ML: 0.5726 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.687
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3238 416 4.8 %
Rwork0.2676 8258 -
obs0.2704 8674 86.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.45 Å2
Refinement stepCycle: LAST / Resolution: 3.31→54.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4362 0 28 15 4405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01234500
X-RAY DIFFRACTIONf_angle_d1.55086131
X-RAY DIFFRACTIONf_chiral_restr0.2213700
X-RAY DIFFRACTIONf_plane_restr0.0115775
X-RAY DIFFRACTIONf_dihedral_angle_d16.12231599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.31-3.780.40091000.33352089X-RAY DIFFRACTION67.23
3.78-4.770.35641450.26272917X-RAY DIFFRACTION93.47
4.77-54.610.28741710.25243252X-RAY DIFFRACTION99.39

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