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- PDB-7jtf: Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from... -

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Basic information

Entry
Database: PDB / ID: 7jtf
TitleStructure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to broadly neutralizing antibody RM2-01
Components
  • Envelope glycoprotein E2
  • RM2-01 Fab heavy chain
  • RM2-01 Fab light chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / HCV / broadly neutralizing antibodies / bNAbs / E2 core / IGHV1-69 / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / : / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / lipid droplet ...host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / : / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / lipid droplet / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / induction by virus of host autophagy / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Hepatitis C virus core protein, chain A superfamily / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus non-structural protein NS4b ...Hepatitis C virus core protein, chain A superfamily / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepatitis C virus, Non-structural 5a protein / Hepatitis C virus, Non-structural 5a protein, domain 1a / Hepatitis C virus non-structural 5a, 1B domain / NS5A domain 1a superfamily / Hepatitis C virus non-structural 5a protein membrane anchor / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / 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 / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / DEAD box, Flavivirus / Flavivirus DEAD domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesMacaca mulatta (Rhesus monkey)
Recombinant Hepatitis C virus HK6a/JFH-1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsTzarum, N. / Wilson, I.A. / Law, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)Al123365 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)Al106005 United States
CitationJournal: Immunity / Year: 2021
Title: HCV Env immunization elicits a rapid VH1-69-like broadly neutralizing antibody response in rhesus macaques
Authors: Tzarum, N. / Chen, F. / Lin, X. / Giang, E. / Velazquez-Moctezuma, R. / Augestad, E.H. / Nagy, K. / He, L. / Davidson, E. / Chavez, D. / Prentoe, J. / Stanfield, R.L. / Lanford, R. / Bukh, J. ...Authors: Tzarum, N. / Chen, F. / Lin, X. / Giang, E. / Velazquez-Moctezuma, R. / Augestad, E.H. / Nagy, K. / He, L. / Davidson, E. / Chavez, D. / Prentoe, J. / Stanfield, R.L. / Lanford, R. / Bukh, J. / Wilson, I.A. / Zhu, J. / Law, M.
History
DepositionAug 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RM2-01 Fab heavy chain
B: RM2-01 Fab light chain
E: Envelope glycoprotein E2
C: RM2-01 Fab heavy chain
D: RM2-01 Fab light chain
F: Envelope glycoprotein E2


Theoretical massNumber of molelcules
Total (without water)136,5256
Polymers136,5256
Non-polymers00
Water0
1
A: RM2-01 Fab heavy chain
B: RM2-01 Fab light chain
E: Envelope glycoprotein E2


Theoretical massNumber of molelcules
Total (without water)68,2633
Polymers68,2633
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-35 kcal/mol
Surface area27140 Å2
MethodPISA
2
C: RM2-01 Fab heavy chain
D: RM2-01 Fab light chain
F: Envelope glycoprotein E2


Theoretical massNumber of molelcules
Total (without water)68,2633
Polymers68,2633
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-36 kcal/mol
Surface area26980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.732, 64.887, 145.208
Angle α, β, γ (deg.)90.000, 105.155, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Antibody RM2-01 Fab heavy chain


Mass: 24107.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody RM2-01 Fab light chain


Mass: 23447.971 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#3: Protein Envelope glycoprotein E2


Mass: 20707.395 Da / Num. of mol.: 2 / 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) / References: UniProt: B9V0E2

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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: 2.99 Å3/Da / Density % sol: 58.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% PEG 400, 0.1M Cadmium chloride, 0.1M sodium acetate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.35→30 Å / Num. obs: 21566 / % possible obs: 91.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 101.57 Å2 / CC1/2: 0.96 / Net I/σ(I): 16.2
Reflection shellResolution: 3.35→3.41 Å / Num. unique obs: 631 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
Blu-Icedata collection
PHASERphasing
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BKB

6bkb


Resolution: 3.35→29.86 Å / SU ML: 0.5108 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 34.1333
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2959 1077 5 %
Rwork0.2423 20443 -
obs0.2449 21520 91.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 117.3 Å2
Refinement stepCycle: LAST / Resolution: 3.35→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8617 0 0 0 8617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00198824
X-RAY DIFFRACTIONf_angle_d0.449112003
X-RAY DIFFRACTIONf_chiral_restr0.04261365
X-RAY DIFFRACTIONf_plane_restr0.00431519
X-RAY DIFFRACTIONf_dihedral_angle_d14.2051194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.50.3564710.3251642X-RAY DIFFRACTION59.13
3.5-3.690.32021130.31482209X-RAY DIFFRACTION79.2
3.69-3.920.39751440.30452588X-RAY DIFFRACTION93.24
3.92-4.220.32781540.27252730X-RAY DIFFRACTION98.53
4.22-4.640.27631250.22842819X-RAY DIFFRACTION99.46
4.64-5.310.2761650.20892767X-RAY DIFFRACTION99.83
5.31-6.670.31861680.24112788X-RAY DIFFRACTION99.97
6.68-29.860.24491370.21692900X-RAY DIFFRACTION99.18

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