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- PDB-1n64: Crystal structure analysis of the immunodominant antigenic site o... -

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Basic information

Entry
Database: PDB / ID: 1n64
TitleCrystal structure analysis of the immunodominant antigenic site on Hepatitis C virus protein bound to mAb 19D9D6
Components
  • Fab 19D9D6 heavy chain
  • Fab 19D9D6 light chain
  • Genome polyprotein Capsid protein C
KeywordsIMMUNE SYSTEM / ANTIBODY PEPTIDE COMPLEX
Function / homology
Function and homology information


hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated transformation of host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / negative regulation of DNA-binding transcription factor activity / 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 / SH3 domain binding ...hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated transformation of host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / negative regulation of DNA-binding transcription factor activity / 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 / SH3 domain binding / nucleoside-triphosphate phosphatase / channel activity / viral nucleocapsid / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by 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 / 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 / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / ATP hydrolysis 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 / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsMenez, R. / Bossus, M. / Muller, B. / Sibai, G. / Dalbon, P. / Ducancel, F. / Jolivet-Reynaud, C. / Stura, E.
CitationJournal: J.Immunol. / Year: 2003
Title: Crystal structure of a hydrophobic immunodominant antigenic site on hepatitis C virus core protein complexed to monoclonal antibody 19D9D6.
Authors: Menez, R. / Bossus, M. / Muller, B.H. / Sibai, G. / Dalbon, P. / Ducancel, F. / Jolivet-Reynaud, C. / Stura, E.A.
History
DepositionNov 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 18, 2013Group: Source and taxonomy
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab 19D9D6 light chain
H: Fab 19D9D6 heavy chain
P: Genome polyprotein Capsid protein C


Theoretical massNumber of molelcules
Total (without water)49,5383
Polymers49,5383
Non-polymers00
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-36 kcal/mol
Surface area20680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.18, 101.7, 55.18
Angle α, β, γ (deg.)90, 98.7, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab 19D9D6 light chain


Mass: 24334.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Fab 19D9D6 heavy chain


Mass: 23563.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (natural) Mus musculus (house mouse)
#3: Protein/peptide Genome polyprotein Capsid protein C / HCV core 13-40 peptide / Core protein / P22


Mass: 1640.929 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SEQUENCE FROM HEPATITIS C VIRUS CORE PROTEIN
References: UniProt: P29846, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, hepacivirin, RNA-directed RNA polymerase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 10% MPEG 5000, 250mM NaCl, 50mM Tris-Hcl, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Method: unknown / Details: Stura, E.A., (2001) J. Crystal Growth, 232, 545.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.009112 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 30, 2001 / Details: mirrors
RadiationMonochromator: Sagitally Focused Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009112 Å / Relative weight: 1
ReflectionResolution: 2.34→20 Å / Num. all: 19408 / Num. obs: 19303 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.071 / Rsym value: 0.067 / Net I/σ(I): 9.2
Reflection shellResolution: 2.34→2.39 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 1179 / Rsym value: 0.233 / % possible all: 91.3
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 14779 / % possible obs: 98.8 % / Num. measured all: 17893 / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 91.3 % / Rmerge(I) obs: 0.233

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1UCB; 1DBA; 1HIL

1ucb

1dba

1hil


Resolution: 2.34→20 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 724 -RANDOM
Rwork0.19 ---
all0.216 17893 --
obs0.268 14779 92.2 %-
Displacement parametersBiso mean: 36.44 Å2
Refinement stepCycle: LAST / Resolution: 2.34→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3484 0 0 202 3686
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0065
X-RAY DIFFRACTIONc_angle_deg1.4
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.34 Å / Lowest resolution: 2.39 Å / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.216

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