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- PDB-6bzy: Structure of the Hepatitis C virus envelope glycoprotein E2 antig... -

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Basic information

Entry
Database: PDB / ID: 6bzy
TitleStructure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423 bound to the 22D11 broadly neutralizing antibody
Components
  • 22D11 Heavy Chain
  • 22D11 Light Chain
  • E2 AS412 peptide
KeywordsIMMUNE SYSTEM / Hepatitis C virus / antibodies / broadly neutralizing antibodies / rational vaccine design / AS412 / E2 / VIRAL PROTEIN
Function / homology
Function and homology information


positive regulation of hexokinase activity / symbiont-mediated perturbation of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / hepacivirin / TBC/RABGAPs / host cell mitochondrial membrane / host cell lipid droplet ...positive regulation of hexokinase activity / symbiont-mediated perturbation of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / hepacivirin / TBC/RABGAPs / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated transformation of host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / positive regulation of cytokinesis / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / negative regulation of protein secretion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / endoplasmic reticulum-Golgi intermediate compartment membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / SH3 domain binding / kinase binding / nucleoside-triphosphate phosphatase / channel activity / viral nucleocapsid / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / entry receptor-mediated virion attachment to host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / 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 / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding
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 / helicase superfamily c-terminal 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 / Immunoglobulins / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Hepacivirus C
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTzarum, N. / Aleman, F. / 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)AI106005 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI123365 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Immunogenetic and structural analysis of a class of HCV broadly neutralizing antibodies and their precursors.
Authors: Aleman, F. / Tzarum, N. / Kong, L. / Nagy, K. / Zhu, J. / Wilson, I.A. / Law, M.
History
DepositionDec 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 2, 2022Group: Database references / Structure summary / Category: audit_author / database_2
Item: _audit_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: 22D11 Heavy Chain
L: 22D11 Light Chain
B: E2 AS412 peptide


Theoretical massNumber of molelcules
Total (without water)49,0773
Polymers49,0773
Non-polymers00
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-35 kcal/mol
Surface area18920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.429, 79.850, 126.936
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody 22D11 Heavy Chain


Mass: 23612.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody 22D11 Light Chain


Mass: 23909.400 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein/peptide E2 AS412 peptide


Mass: 1554.710 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepacivirus C / Production host: Homo sapiens (human) / References: UniProt: P27958*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 8000, 0.1 M sodium chloride, 0.1 M CAPS pH 10.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 62992 / % possible obs: 99.7 % / Redundancy: 6.8 % / Net I/σ(I): 41.8
Reflection shellResolution: 1.6→1.63 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BZU

6bzu


Resolution: 1.6→40.137 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.27
RfactorNum. reflection% reflection
Rfree0.2184 3046 4.84 %
Rwork0.1883 --
obs0.1898 62911 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→40.137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3364 0 0 461 3825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063455
X-RAY DIFFRACTIONf_angle_d0.864716
X-RAY DIFFRACTIONf_dihedral_angle_d13.1832051
X-RAY DIFFRACTIONf_chiral_restr0.053530
X-RAY DIFFRACTIONf_plane_restr0.006599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6250.31911230.2652639X-RAY DIFFRACTION99
1.625-1.65170.25161240.25892718X-RAY DIFFRACTION100
1.6517-1.68010.27811450.23722669X-RAY DIFFRACTION100
1.6801-1.71070.23651510.22812706X-RAY DIFFRACTION100
1.7107-1.74360.25461360.21282690X-RAY DIFFRACTION100
1.7436-1.77920.25121370.20692685X-RAY DIFFRACTION100
1.7792-1.81790.22451410.19952635X-RAY DIFFRACTION98
1.8179-1.86020.22791330.20212705X-RAY DIFFRACTION100
1.8602-1.90670.2481260.20562701X-RAY DIFFRACTION100
1.9067-1.95820.22551450.20862703X-RAY DIFFRACTION100
1.9582-2.01590.21831690.19642687X-RAY DIFFRACTION100
2.0159-2.08090.23431450.19692681X-RAY DIFFRACTION100
2.0809-2.15530.21491330.18482713X-RAY DIFFRACTION100
2.1553-2.24160.20181280.18952710X-RAY DIFFRACTION99
2.2416-2.34360.23331270.20212737X-RAY DIFFRACTION100
2.3436-2.46710.23591440.20222722X-RAY DIFFRACTION100
2.4671-2.62170.24281220.19822759X-RAY DIFFRACTION100
2.6217-2.8240.21881260.21032732X-RAY DIFFRACTION99
2.824-3.10810.24131470.1982762X-RAY DIFFRACTION100
3.1081-3.55770.24651510.18262776X-RAY DIFFRACTION100
3.5577-4.48130.17161300.15852800X-RAY DIFFRACTION100
4.4813-40.14980.18391630.16232935X-RAY DIFFRACTION100

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