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- PDB-2f1s: Crystal Structure of a Viral FLIP MC159 -

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Basic information

Entry
Database: PDB / ID: 2f1s
TitleCrystal Structure of a Viral FLIP MC159
ComponentsViral CASP8 and FADD-like apoptosis regulator
KeywordsAPOPTOSIS / FLIP / DED / death receptor signaling / DISC / caspase activation
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
Viral CASP8 and FADD-like apoptosis regulator
Similarity search - Component
Biological speciesMolluscum contagiosum virus subtype 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsLi, F.-Y. / Jeffrey, P.D. / Yu, J.W. / Shi, Y.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal Structure of a Viral FLIP: INSIGHTS INTO FLIP-MEDIATED INHIBITION OF DEATH RECEPTOR SIGNALING.
Authors: Li, F.-Y. / Jeffrey, P.D. / Yu, J.W. / Shi, Y.
History
DepositionNov 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2005Provider: 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


Theoretical massNumber of molelcules
Total (without water)20,7951
Polymers20,7951
Non-polymers00
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.859, 63.271, 76.360
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: 20794.992 Da / Num. of mol.: 1
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: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q98325
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.024 Å3/Da / Density % sol: 39.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 2000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979, 0.9794, 0.98, 0.9641
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97941
30.981
40.96411
ReflectionResolution: 1.4→50 Å / Num. all: 34179 / Num. obs: 33495 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.4→1.45 Å / % possible all: 93

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.4→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.236 1576 random
Rwork0.206 --
all0.207 34179 -
obs0.206 31044 -
Refinement stepCycle: LAST / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1376 0 0 174 1550
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.62
X-RAY DIFFRACTIONc_bond_d0.014

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