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- PDB-2bbz: Crystal Structure of MC159 Reveals Molecular Mechanism of DISC As... -

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Basic information

Entry
Database: PDB / ID: 2bbz
TitleCrystal Structure of MC159 Reveals Molecular Mechanism of DISC Assembly and vFLIP Inhibition
ComponentsViral CASP8 and FADD-like apoptosis regulator
KeywordsVIRAL PROTEIN / death effector domain
Function / homology
Function and homology information


Caspase activation via Death Receptors in the presence of ligand / symbiont-mediated suppression of host autophagy / symbiont-mediated suppression of host apoptosis / positive regulation of necroptotic process / negative regulation of apoptotic signaling pathway / symbiont-mediated suppression of host NF-kappaB cascade / host cell cytoplasm / host cell nucleus
Similarity search - Function
Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Death Domain, Fas / Death Domain, Fas / Death-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Viral CASP8 and FADD-like apoptosis regulator
Similarity search - Component
Biological speciesMolluscum contagiosum virus subtype 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.8 Å
AuthorsYang, J.K. / Wang, L. / Zheng, L. / Wan, F. / Ahmed, M. / Lenardo, M.J. / Wu, H.
CitationJournal: Mol.Cell / Year: 2005
Title: Crystal structure of MC159 reveals molecular mechanism of DISC assembly and FLIP inhibition.
Authors: Yang, J.K. / Wang, L. / Zheng, L. / Wan, F. / Ahmed, M. / Lenardo, M.J. / Wu, H.
History
DepositionOct 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Viral CASP8 and FADD-like apoptosis regulator
B: Viral CASP8 and FADD-like apoptosis regulator
C: Viral CASP8 and FADD-like apoptosis regulator
D: Viral CASP8 and FADD-like apoptosis regulator


Theoretical massNumber of molelcules
Total (without water)112,1564
Polymers112,1564
Non-polymers00
Water93752
1
A: Viral CASP8 and FADD-like apoptosis regulator


Theoretical massNumber of molelcules
Total (without water)28,0391
Polymers28,0391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Viral CASP8 and FADD-like apoptosis regulator


Theoretical massNumber of molelcules
Total (without water)28,0391
Polymers28,0391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Viral CASP8 and FADD-like apoptosis regulator


Theoretical massNumber of molelcules
Total (without water)28,0391
Polymers28,0391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Viral CASP8 and FADD-like apoptosis regulator


Theoretical massNumber of molelcules
Total (without water)28,0391
Polymers28,0391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.857, 108.065, 142.643
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein
Viral CASP8 and FADD-like apoptosis regulator / v-CFLAR / Viral FLICE-inhibitory protein / v-FLIP


Mass: 28038.932 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Molluscum contagiosum virus subtype 1 / Genus: Molluscipoxvirus / Species: Molluscum contagiosum virus / Strain: subtype 1 / Plasmid: modified pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus RIPL / References: UniProt: Q98325
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.88 Å3/Da / Density % sol: 57.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 50-150 mM sodium/potassium phosphate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9795 Å
DetectorDetector: CCD / Date: Sep 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.8→30 Å / Num. all: 13309 / Num. obs: 13309 / % possible obs: 99.7 % / Observed criterion σ(I): -3
Reflection shellResolution: 3.8→3.94 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: SAD / Resolution: 3.8→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.372 1264 random
Rwork0.325 --
obs0.325 12440 -
all-12440 -
Refinement stepCycle: LAST / Resolution: 3.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5964 0 0 52 6016
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.273

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