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

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Basic information

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


symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated suppression of host apoptosis / Caspase activation via Death Receptors in the presence of ligand / suppression by virus of host autophagy / positive regulation of necroptotic process / negative regulation of apoptotic signaling pathway / 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
AZIDE ION / Viral CASP8 and FADD-like apoptosis regulator
Similarity search - Component
Biological speciesMolluscum contagiosum virus subtype 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 17, 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 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2132
Polymers22,1711
Non-polymers421
Water5,747319
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.979, 62.867, 75.806
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: Protein Viral CASP8 and FADD-like apoptosis regulator / v-CFLAR / Viral FLICE-inhibitory protein / v-FLIP


Mass: 22170.553 Da / Num. of mol.: 1 / Fragment: death effector domain (residues 1-187)
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: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 1.88 Å3/Da / Density % sol: 34.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.0 - 1.2 M sodium acetate, 0.1 M imidazole , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.2→15 Å / Num. all: 52241 / Num. obs: 52241 / % possible obs: 99.6 % / Observed criterion σ(I): -3
Reflection shellResolution: 1.2→1.24 Å / % possible all: 97.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2BBZ

2bbz


Resolution: 1.2→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.226 5154 Random
Rwork0.211 --
obs0.211 50964 -
all-52241 -
Refinement stepCycle: LAST / Resolution: 1.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1492 0 3 319 1814
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1

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