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- PDB-3h13: c-FLIPL protease-like domain -

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Basic information

Entry
Database: PDB / ID: 3h13
Titlec-FLIPL protease-like domain
ComponentsCASP8 and FADD-like apoptosis regulator
KeywordsAPOPTOSIS / cFLIP-L / dimer / cell death / Alternative splicing / Host-virus interaction / Polymorphism
Function / homology
Function and homology information


negative regulation of myoblast fusion / skeletal myofibril assembly / skeletal muscle atrophy / TRAIL signaling / CD95 death-inducing signaling complex / regulation of skeletal muscle satellite cell proliferation / ripoptosome / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 ...negative regulation of myoblast fusion / skeletal myofibril assembly / skeletal muscle atrophy / TRAIL signaling / CD95 death-inducing signaling complex / regulation of skeletal muscle satellite cell proliferation / ripoptosome / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / regulation of necroptotic process / positive regulation of extracellular matrix organization / skeletal muscle tissue regeneration / positive regulation of glomerular mesangial cell proliferation / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / death-inducing signaling complex / negative regulation of hepatocyte apoptotic process / cysteine-type endopeptidase activity involved in execution phase of apoptosis / death receptor binding / positive regulation of hepatocyte proliferation / negative regulation of cellular response to transforming growth factor beta stimulus / execution phase of apoptosis / RIPK1-mediated regulated necrosis / negative regulation of cardiac muscle cell apoptotic process / response to testosterone / cellular response to nitric oxide / negative regulation of reactive oxygen species biosynthetic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / skeletal muscle tissue development / keratinocyte differentiation / enzyme activator activity / cellular response to epidermal growth factor stimulus / cellular response to dexamethasone stimulus / erythrocyte differentiation / cellular response to estradiol stimulus / negative regulation of extrinsic apoptotic signaling pathway / Regulation of TNFR1 signaling / wound healing / neuron differentiation / positive regulation of neuron projection development / cellular response to insulin stimulus / positive regulation of neuron apoptotic process / positive regulation of NF-kappaB transcription factor activity / cellular response to hypoxia / positive regulation of canonical NF-kappaB signal transduction / protease binding / positive regulation of ERK1 and ERK2 cascade / apoptotic process / protein-containing complex binding / negative regulation of apoptotic process / proteolysis / cytoplasm / cytosol
Similarity search - Function
Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Rossmann fold - #1460 / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : ...Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Rossmann fold - #1460 / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Death-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CASP8 and FADD-like apoptosis regulator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJeffrey, P.D. / Yu, J.W. / Shi, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Mechanism of procaspase-8 activation by c-FLIPL.
Authors: Yu, J.W. / Jeffrey, P.D. / Shi, Y.
History
DepositionApr 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CASP8 and FADD-like apoptosis regulator


Theoretical massNumber of molelcules
Total (without water)31,4501
Polymers31,4501
Non-polymers00
Water1,36976
1
A: CASP8 and FADD-like apoptosis regulator

A: CASP8 and FADD-like apoptosis regulator


Theoretical massNumber of molelcules
Total (without water)62,9002
Polymers62,9002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Unit cell
Length a, b, c (Å)101.940, 101.940, 61.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein CASP8 and FADD-like apoptosis regulator


Mass: 31450.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFLAR, CASH, CASP8AP1, CLARP, MRIT / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15519
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THIS SEQUENCE DISCREPANCY MAY BE DUE TO VARIATIONS AMONG DIFFERENT CONSTRUCTS IN ...AUTHORS STATE THAT THIS SEQUENCE DISCREPANCY MAY BE DUE TO VARIATIONS AMONG DIFFERENT CONSTRUCTS IN THE DATABASES. RESIDUE 369 IS ASN IN GENBANK ENTRY CAA74366.1

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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: 2.93 Å3/Da / Density % sol: 57.97 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Mes, 18% PEG, 5000 monomethyl ether, 0.1 M ammonium sulfate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. all: 19006 / Num. obs: 19006 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 23.7 Å2 / Rsym value: 0.068 / Net I/σ(I): 19.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 6.8 / Num. unique all: 1872 / Rsym value: 0.395 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.43 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1402184.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.22 956 5.2 %RANDOM
Rwork0.187 ---
obs0.187 18283 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.9337 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 36.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å20 Å2
2---1.64 Å20 Å2
3---3.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 0 0 76 1780
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.542.5
X-RAY DIFFRACTIONc_mcangle_it3.613
X-RAY DIFFRACTIONc_scbond_it3.683
X-RAY DIFFRACTIONc_scangle_it5.253.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.219 151 5.3 %
Rwork0.185 2717 -
obs--92 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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