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- PDB-7mwx: Structure of the core ectodomain of the hepatitis C virus envelop... -

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Basic information

Entry
Database: PDB / ID: 7mwx
TitleStructure of the core ectodomain of the hepatitis C virus envelope glycoprotein 2 with tamarin CD81
Components
  • 2A12 Fab Heavy Chain
  • 2A12 Fab Light Chain
  • CD81 protein
  • Core protein precursor eE2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Glycoprotein / Receptor / Viral protein / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


: / CD4-positive, alpha-beta T cell costimulation / osteoclast fusion / positive regulation of B cell receptor signaling pathway / myoblast fusion involved in skeletal muscle regeneration / positive regulation of inflammatory response to antigenic stimulus / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of macrophage migration / macrophage fusion / immunological synapse formation ...: / CD4-positive, alpha-beta T cell costimulation / osteoclast fusion / positive regulation of B cell receptor signaling pathway / myoblast fusion involved in skeletal muscle regeneration / positive regulation of inflammatory response to antigenic stimulus / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of macrophage migration / macrophage fusion / immunological synapse formation / positive regulation of T-helper 2 cell cytokine production / tetraspanin-enriched microdomain / positive regulation of B cell activation / positive regulation of protein exit from endoplasmic reticulum / humoral immune response mediated by circulating immunoglobulin / positive regulation of CD4-positive, alpha-beta T cell proliferation / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / cholesterol binding / positive regulation of T cell receptor signaling pathway / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / host cell mitochondrion / cellular response to low-density lipoprotein particle stimulus / immunological synapse / positive regulation of receptor clustering / 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 localization to plasma membrane / protein localization / receptor internalization / positive regulation of peptidyl-tyrosine phosphorylation / integrin binding / protein complex oligomerization / monoatomic ion channel activity / basolateral plasma membrane / viral nucleocapsid / positive regulation of MAPK cascade / 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 / symbiont entry into host cell / induction by virus of host autophagy / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / positive regulation of cell population proliferation / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Tetraspanin, conserved site / Transmembrane 4 family signature. / Tetraspanin, animals / Tetraspanin, EC2 domain superfamily / Tetraspanin/Peripherin / Tetraspanin family / : / Hepatitis C virus core protein, chain A superfamily / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily ...Tetraspanin, conserved site / Transmembrane 4 family signature. / Tetraspanin, animals / Tetraspanin, EC2 domain superfamily / Tetraspanin/Peripherin / Tetraspanin family / : / 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
Genome polyprotein / CD81 protein
Similarity search - Component
Biological speciesHepacivirus C
Mus musculus (house mouse)
Saguinus oedipus (cotton-top tamarin)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Core protein precursor eE2
G: Core protein precursor eE2
A: 2A12 Fab Heavy Chain
B: 2A12 Fab Light Chain
D: CD81 protein
E: 2A12 Fab Heavy Chain
F: 2A12 Fab Light Chain
H: CD81 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,22413
Polymers173,5498
Non-polymers1,6755
Water00
1
C: Core protein precursor eE2
A: 2A12 Fab Heavy Chain
B: 2A12 Fab Light Chain
D: CD81 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8047
Polymers86,7754
Non-polymers1,0293
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Core protein precursor eE2
E: 2A12 Fab Heavy Chain
F: 2A12 Fab Light Chain
H: CD81 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4206
Polymers86,7754
Non-polymers6462
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.954, 127.774, 212.374
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules CGDH

#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: 29314.105 Da / Num. of mol.: 2 / Fragment: DeltaHVR1
Source method: isolated from a genetically manipulated source
Details: J6 genotype / Source: (gene. exp.) Hepacivirus C / Cell line (production host): HEK293 gnti- cells / Production host: Homo sapiens (human)
References: UniProt: A0A2I6PIY1, RNA-directed RNA polymerase, hepacivirin, nucleoside-triphosphate phosphatase, RNA helicase
#4: Protein CD81 protein


Mass: 10141.375 Da / Num. of mol.: 2 / Fragment: second extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saguinus oedipus (cotton-top tamarin) / Gene: CD81 / Cell line (production host): HEK293 GNTI- cells / Production host: Homo sapiens (human) / References: UniProt: Q9N0J9

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Antibody , 2 types, 4 molecules AEBF

#2: Antibody 2A12 Fab Heavy Chain


Mass: 23207.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody 2A12 Fab Light Chain


Mass: 24111.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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Sugars , 3 types, 5 molecules

#5: 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
#6: 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
#7: 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: isolated from a genetically manipulated source
Formula: C8H15NO6
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 interestN

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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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.2M sodium acetate pH 4.5, 4% v/v tacsimate pH 4.0, 12% v/v PEG Smear Medium

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.32→54.74 Å / Num. obs: 31609 / % possible obs: 99.5 % / Redundancy: 13.2 % / CC1/2: 0.99 / Net I/σ(I): 6.8
Reflection shellResolution: 3.32→3.5 Å / Num. unique obs: 4559 / CC1/2: 0.39

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Processing

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

4web


Resolution: 3.32→53.093 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 33.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2831 1590 5.04 %
Rwork0.2392 --
obs0.2414 31528 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.32→53.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10350 0 109 0 10459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210752
X-RAY DIFFRACTIONf_angle_d0.66814746
X-RAY DIFFRACTIONf_dihedral_angle_d4.5086406
X-RAY DIFFRACTIONf_chiral_restr0.0451720
X-RAY DIFFRACTIONf_plane_restr0.0051876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3202-3.42730.4331320.37342674X-RAY DIFFRACTION100
3.4273-3.54980.36431410.33372724X-RAY DIFFRACTION100
3.5498-3.69190.39221260.30632623X-RAY DIFFRACTION97
3.6919-3.85990.36981490.26972700X-RAY DIFFRACTION100
3.8599-4.06330.31251420.24242710X-RAY DIFFRACTION100
4.0633-4.31780.27111540.19122690X-RAY DIFFRACTION100
4.3178-4.6510.23241510.17552703X-RAY DIFFRACTION100
4.651-5.11870.23321460.18182752X-RAY DIFFRACTION100
5.1187-5.85850.26311510.19812700X-RAY DIFFRACTION99
5.8585-7.3780.29041510.28632773X-RAY DIFFRACTION100
7.378-530.27151470.24112889X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -13.9078 Å / Origin y: 16.0699 Å / Origin z: -28.4282 Å
111213212223313233
T1.0021 Å20.1469 Å2-0.0286 Å2-0.9044 Å20.038 Å2--0.9289 Å2
L0.2482 °20.3166 °2-0.096 °2-1.2885 °20.2554 °2--1.3515 °2
S-0.0406 Å °-0.1823 Å °0.0663 Å °0.1825 Å °-0.0937 Å °-0.0846 Å °-0.0896 Å °-0.0718 Å °0.109 Å °
Refinement TLS groupSelection details: all

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