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- PDB-7mww: Structure of hepatitis C virus envelope full-length glycoprotein ... -

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Basic information

Entry
Database: PDB / ID: 7mww
TitleStructure of hepatitis C virus envelope full-length glycoprotein 2 (eE2) from J6 genotype
Components
  • 2A12 Fab Heavy chain
  • 2A12 Fab light chain
  • Core protein precursor eE2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Glycoprotein / Viral protein / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated transformation of host cell / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / host cell mitochondrion / 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 / channel activity / viral nucleocapsid ...host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated transformation of host cell / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / host cell mitochondrion / 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 / channel activity / viral nucleocapsid / monoatomic ion transmembrane transport / 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 / symbiont entry into host cell / ribonucleoprotein complex / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
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 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 core protein, chain A superfamily / : / 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 / NS3 RNA helicase, C-terminal helical domain / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesHepacivirus C
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsKumar, A. / Hossain, R.A. / Yost, S.A. / Bu, W. / Wang, Y. / Dearborn, A.D. / Grakoui, A. / Cohen, J.I. / Marcotrigiano, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nature / Year: 2021
Title: Structural insights into hepatitis C virus receptor binding and entry.
Authors: Kumar, A. / Hossain, R.A. / Yost, S.A. / Bu, W. / Wang, Y. / Dearborn, A.D. / Grakoui, A. / Cohen, J.I. / Marcotrigiano, J.
History
DepositionMay 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Core protein precursor eE2
H: 2A12 Fab Heavy chain
L: 2A12 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9857
Polymers80,5323
Non-polymers1,4534
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-7 kcal/mol
Surface area29410 Å2
Unit cell
Length a, b, c (Å)95.840, 155.561, 129.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody 2A12 Fab Heavy chain


Mass: 23462.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody 2A12 Fab light chain


Mass: 26553.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

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Protein / Non-polymers , 2 types, 103 molecules E

#1: Protein Core protein precursor eE2 / Envelope glycoprotein E1 / Envelope glycoprotein E2 / Genome polyprotein / Gp32 / Hepacivirin / ...Envelope glycoprotein E1 / Envelope glycoprotein E2 / Genome polyprotein / Gp32 / Hepacivirin / Mature core protein / NS1 / NS3 helicase / NS3 protease / NS3P / NS5B / Non-structural protein 4A / Non-structural protein 4B / Non-structural protein 5A / Protease NS2 / RNA-directed RNA polymerase / Serine protease/helicase NS3 / Viroporin p7 / Viroporin p70 / gp35 / gp68 / gp70 / p21 / p23 / p27 / p56/58 / p68 / p8


Mass: 30515.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: J6 genotype / Source: (gene. exp.) Hepacivirus C / Cell line (production host): HEK293T GnTI- cells / Production host: Homo sapiens (human) / Tissue (production host): Liver
References: UniProt: A0A2I6PIY1, RNA-directed RNA polymerase, hepacivirin, nucleoside-triphosphate phosphatase, RNA helicase
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 3 types, 4 molecules

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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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-Glycam 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
[]{[(4+1)][b-D-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: isolated from a genetically manipulated source
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: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 4% v/v tacsimate pH 5.0, 14% w/v PEG3350, and 4% D-(+)-trehalose dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.71→33.34 Å / Num. obs: 49955 / % possible obs: 99.01 % / Redundancy: 1.98 % / Biso Wilson estimate: 35.82 Å2 / CC1/2: 0.98 / Net I/σ(I): 6.3
Reflection shellResolution: 2.71→2.807 Å / Num. unique obs: 2583 / CC1/2: 0.48

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Coot0.8.9.2 ELmodel building
MOSFLM7.2.2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WEB

4web


Resolution: 2.71→33.334 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0.26 / Phase error: 26.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2702 2458 4.92 %
Rwork0.218 --
obs0.2205 49955 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.71→33.334 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4605 0 95 102 4802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054859
X-RAY DIFFRACTIONf_angle_d0.8476660
X-RAY DIFFRACTIONf_dihedral_angle_d3.3662819
X-RAY DIFFRACTIONf_chiral_restr0.047766
X-RAY DIFFRACTIONf_plane_restr0.007838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.76210.34871450.30992575X-RAY DIFFRACTION96
2.7621-2.81850.3851310.31742602X-RAY DIFFRACTION97
2.8185-2.87970.37541720.30272579X-RAY DIFFRACTION98
2.8797-2.94670.40421500.29592611X-RAY DIFFRACTION97
2.9467-3.02030.29721320.27842612X-RAY DIFFRACTION98
3.0203-3.10190.3091240.27292655X-RAY DIFFRACTION98
3.1019-3.19310.32721630.27072611X-RAY DIFFRACTION99
3.1931-3.29610.34521350.24832657X-RAY DIFFRACTION99
3.2961-3.41380.29881610.24672610X-RAY DIFFRACTION99
3.4138-3.55030.2851470.22372654X-RAY DIFFRACTION99
3.5503-3.71170.27021120.20932661X-RAY DIFFRACTION99
3.7117-3.90710.26791510.19992626X-RAY DIFFRACTION99
3.9071-4.15150.24771390.18412680X-RAY DIFFRACTION99
4.1515-4.47130.20721140.16582656X-RAY DIFFRACTION99
4.4713-4.920.16371270.14892660X-RAY DIFFRACTION99
4.92-5.6290.19671020.16732714X-RAY DIFFRACTION99
5.629-7.08070.20111110.20732668X-RAY DIFFRACTION99
7.0807-33.330.22381420.20162666X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 24.788 Å / Origin y: 26.6205 Å / Origin z: -13.4119 Å
111213212223313233
T0.1856 Å20.0304 Å20.0212 Å2-0.1631 Å20.0641 Å2--0.1471 Å2
L1.075 °2-0.0348 °20.0118 °2-0.6434 °20.2709 °2--2.4534 °2
S-0.0222 Å °0.0631 Å °-0.2254 Å °-0.0808 Å °-0.0998 Å °-0.0486 Å °0.4839 Å °-0.0436 Å °0.0482 Å °
Refinement TLS groupSelection details: all

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