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- PDB-1xct: Complex HCV core-Fab 19D9D6-Protein L mutant (D55A, L57H, Y64W) i... -

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Basic information

Entry
Database: PDB / ID: 1xct
TitleComplex HCV core-Fab 19D9D6-Protein L mutant (D55A, L57H, Y64W) in space group P21212
Components
  • Capsid protein C
  • Monoclonal antibody 19D9D6 Heavy chain
  • Monoclonal antibody 19D9D6 Light chain
  • Protein L
KeywordsIMMUNE SYSTEM / Crystal packing / Fab / protein L / peptide complex
Function / homology
Function and homology information


hepacivirin / 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 / SH3 domain binding / : ...hepacivirin / 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 / SH3 domain binding / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / RNA helicase / induction by virus of host autophagy / ribonucleoprotein complex / RNA-directed RNA polymerase / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Ubiquitin-like (UB roll) - #10 / 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 ...Ubiquitin-like (UB roll) - #10 / 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 / Ubiquitin-like (UB roll) / 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. / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Roll / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesFinegoldia magna (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsMenez, R. / Housden, N.G. / Harrison, S. / Jolivet-Reynaud, C. / Gore, M.G. / Stura, E.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Different crystal packing in Fab-protein L semi-disordered peptide complex.
Authors: Menez, R. / Housden, N.G. / Harrison, S. / Jolivet-Reynaud, C. / Gore, M.G. / Stura, E.A.
History
DepositionSep 3, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 31, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Capsid protein C
Q: Capsid protein C
A: Monoclonal antibody 19D9D6 Light chain
B: Monoclonal antibody 19D9D6 Heavy chain
L: Protein L
C: Monoclonal antibody 19D9D6 Light chain
D: Monoclonal antibody 19D9D6 Heavy chain
M: Protein L


Theoretical massNumber of molelcules
Total (without water)123,4208
Polymers123,4208
Non-polymers00
Water6,107339
1
P: Capsid protein C
A: Monoclonal antibody 19D9D6 Light chain
B: Monoclonal antibody 19D9D6 Heavy chain
L: Protein L


Theoretical massNumber of molelcules
Total (without water)61,7104
Polymers61,7104
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Q: Capsid protein C
C: Monoclonal antibody 19D9D6 Light chain
D: Monoclonal antibody 19D9D6 Heavy chain
M: Protein L


Theoretical massNumber of molelcules
Total (without water)61,7104
Polymers61,7104
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.50, 222.48, 43.76
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein/peptide Capsid protein C / / core protein


Mass: 4909.684 Da / Num. of mol.: 2 / Fragment: residues 2-45 / Source method: obtained synthetically / Details: This sequence occurs naturally in HCV virus / References: UniProt: P26661
#2: Antibody Monoclonal antibody 19D9D6 Light chain


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


Mass: 23563.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Protein Protein L /


Mass: 8903.001 Da / Num. of mol.: 2 / Mutation: D55A,L57H,Y64W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Finegoldia magna (bacteria) / Strain: ATCC 29328 / Plasmid: PKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM103
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 8% MPEG 5K, sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 14, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.05→20 Å / Num. all: 22478 / Num. obs: 22370 / % possible obs: 89.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.15 %
Reflection shellHighest resolution: 3.05 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.329 1114 RANDOM
Rwork0.193 --
all0.195 22478 -
obs0.195 22370 -
Refinement stepCycle: LAST / Resolution: 3.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8213 0 0 339 8552

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