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

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Basic information

Entry
Database: PDB / ID: 30bc
TitleStructure of the Hepatitis C Virus E2 Core from Genotype 6a in Complex with Germline Reverted Variants of the Broadly Neutralizing Antibody AR3A
Components
  • (Fab AR3A 1-69 ...) x 2
  • HCV E2 envelope protein
KeywordsVIRAL PROTEIN / Hepatitis C virus / E2 envelope protein / neutralizing antibodies / Germ line
Biological speciesHomo sapiens (human)
Recombinant Hepatitis C virus HK6a/JFH-1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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
H: Fab AR3A 1-69 heavy chain
E: HCV E2 envelope protein
L: Fab AR3A 1-69 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7107
Polymers70,6223
Non-polymers1,0884
Water3,531196
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-18 kcal/mol
Surface area28660 Å2
Unit cell
Length a, b, c (Å)61.428, 66.952, 218.793
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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Antibody , 2 types, 2 molecules HL

#1: Antibody Fab AR3A 1-69 heavy chain


Mass: 24383.281 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 AR3A 1-69 light chain


Mass: 25531.340 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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Protein / Non-polymers , 2 types, 197 molecules E

#2: 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)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 4 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
#5: 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.: 3 / 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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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: 3.19 Å3/Da / Density % sol: 61.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium sulfate 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: 0.96546 Å
DetectorType: DECTRIS PILATUS4 X 4M / Detector: PIXEL / Date: Aug 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.04→46.98 Å / Num. obs: 57518 / % possible obs: 98.8 % / Redundancy: 4 % / Biso Wilson estimate: 50.4 Å2 / CC1/2: 0.99 / Net I/σ(I): 7.2
Reflection shellResolution: 2.08→2.11 Å / Num. unique obs: 2120 / CC1/2: 0.47

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHASERphasing
EDNAdata reduction
EDNAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→46.98 Å / SU ML: 0.3023 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.318
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2811 2732 4.87 %
Rwork0.2351 53350 -
obs0.2372 56082 95.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.09 Å2
Refinement stepCycle: LAST / Resolution: 2.04→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4585 0 70 196 4851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01114819
X-RAY DIFFRACTIONf_angle_d1.30776567
X-RAY DIFFRACTIONf_chiral_restr0.2088740
X-RAY DIFFRACTIONf_plane_restr0.012843
X-RAY DIFFRACTIONf_dihedral_angle_d15.25411730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.080.3772990.35122021X-RAY DIFFRACTION74.05
2.08-2.110.32881120.34122256X-RAY DIFFRACTION81.6
2.11-2.150.34631230.34392555X-RAY DIFFRACTION93.15
2.15-2.20.36621390.34322693X-RAY DIFFRACTION98.27
2.2-2.250.33691480.32992680X-RAY DIFFRACTION99.37
2.25-2.30.381420.30972741X-RAY DIFFRACTION98.97
2.3-2.350.34891440.30592729X-RAY DIFFRACTION99.62
2.36-2.420.35381240.30022759X-RAY DIFFRACTION99.35
2.42-2.490.35231370.28862716X-RAY DIFFRACTION99.03
2.49-2.570.32831330.28692720X-RAY DIFFRACTION97.77
2.57-2.660.29661580.27442725X-RAY DIFFRACTION99.21
2.66-2.770.2971620.26042704X-RAY DIFFRACTION99
2.77-2.890.3231380.26292742X-RAY DIFFRACTION99.21
2.89-3.050.28471350.26832774X-RAY DIFFRACTION99.15
3.05-3.240.33521480.26042745X-RAY DIFFRACTION98.91
3.24-3.490.29721200.24132723X-RAY DIFFRACTION96.67
3.49-3.840.25361280.2232760X-RAY DIFFRACTION98.06
3.84-4.390.24431420.19942768X-RAY DIFFRACTION97.32
4.39-5.530.22191420.18372735X-RAY DIFFRACTION95.96
5.54-46.980.2771580.21222804X-RAY DIFFRACTION93.35

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