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- PDB-2fun: alternative p35-caspase-8 complex -

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Basic information

Entry
Database: PDB / ID: 2fun
Titlealternative p35-caspase-8 complex
Components
  • Early 35 kDa protein
  • caspase-8
KeywordsAPOPTOSIS/HYDROLASE / APOPTOSIS-HYDROLASE complex
Function / homology
Function and homology information


caspase-8 / death effector domain binding / FasL/ CD95L signaling / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / TRAIL signaling / CD95 death-inducing signaling complex / ripoptosome / Defective RIPK1-mediated regulated necrosis / Apoptotic execution phase ...caspase-8 / death effector domain binding / FasL/ CD95L signaling / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / TRAIL signaling / CD95 death-inducing signaling complex / ripoptosome / Defective RIPK1-mediated regulated necrosis / Apoptotic execution phase / TRAIL-activated apoptotic signaling pathway / Activation, myristolyation of BID and translocation to mitochondria / TRIF-mediated programmed cell death / Microbial modulation of RIPK1-mediated regulated necrosis / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TLR3-mediated TICAM1-dependent programmed cell death / symbiont-mediated suppression of host apoptosis / Caspase activation via Death Receptors in the presence of ligand / positive regulation of macrophage differentiation / self proteolysis / response to cobalt ion / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / death-inducing signaling complex / CLEC7A/inflammasome pathway / negative regulation of necroptotic process / response to anesthetic / regulation of tumor necrosis factor-mediated signaling pathway / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / tumor necrosis factor receptor binding / death receptor binding / natural killer cell activation / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / execution phase of apoptosis / regulation of innate immune response / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / : / B cell activation / positive regulation of proteolysis / macrophage differentiation / response to tumor necrosis factor / extrinsic apoptotic signaling pathway via death domain receptors / cysteine-type endopeptidase inhibitor activity / Caspase-mediated cleavage of cytoskeletal proteins / extrinsic apoptotic signaling pathway / negative regulation of canonical NF-kappaB signal transduction / cysteine-type peptidase activity / regulation of cytokine production / protein maturation / proteolysis involved in protein catabolic process / T cell activation / positive regulation of interleukin-1 beta production / Regulation of NF-kappa B signaling / apoptotic signaling pathway / Regulation of TNFR1 signaling / NOD1/2 Signaling Pathway / protein processing / Regulation of necroptotic cell death / cellular response to mechanical stimulus / positive regulation of neuron apoptotic process / response to estradiol / lamellipodium / peptidase activity / heart development / cell body / scaffold protein binding / angiogenesis / response to lipopolysaccharide / response to ethanol / mitochondrial outer membrane / positive regulation of canonical NF-kappaB signal transduction / cytoskeleton / positive regulation of cell migration / positive regulation of apoptotic process / cysteine-type endopeptidase activity / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / negative regulation of apoptotic process / protein-containing complex / mitochondrion / proteolysis / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Baculovirus p35 / Baculovirus p35 / Baculovirus p35, apoptosis preventing protein / Baculovirus p35 superfamily / Apoptosis preventing protein / Caspase-8 / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Death effector domain ...Baculovirus p35 / Baculovirus p35 / Baculovirus p35, apoptosis preventing protein / Baculovirus p35 superfamily / Apoptosis preventing protein / Caspase-8 / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Death effector domain / Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / 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 / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Early 35 kDa protein / Caspase-8
Similarity search - Component
Biological speciesAutographa californica nucleopolyhedrovirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLu, M. / Min, T. / Eliezer, D. / Wu, H.
CitationJournal: Chem.Biol. / Year: 2006
Title: Native chemical ligation in covalent caspase inhibition by p35.
Authors: Lu, M. / Min, T. / Eliezer, D. / Wu, H.
History
DepositionJan 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Early 35 kDa protein
B: caspase-8
C: Early 35 kDa protein
D: caspase-8


Theoretical massNumber of molelcules
Total (without water)128,5304
Polymers128,5304
Non-polymers00
Water46826
1
A: Early 35 kDa protein
B: caspase-8


Theoretical massNumber of molelcules
Total (without water)64,2652
Polymers64,2652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Early 35 kDa protein
D: caspase-8


Theoretical massNumber of molelcules
Total (without water)64,2652
Polymers64,2652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.970, 117.340, 346.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Early 35 kDa protein / p35 / Apoptosis preventing protein


Mass: 34742.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica nucleopolyhedrovirus
Genus: Nucleopolyhedrovirus / Gene: P35 / Production host: Escherichia coli (E. coli) / References: UniProt: P08160
#2: Protein caspase-8


Mass: 29522.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q14790
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.95 Å3/Da / Density % sol: 68.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: VAPOR DIFFUSION, HANGING DROP, pH 7, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→24 Å / Num. obs: 37662 / % possible obs: 91.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1I4E

1i4e


Resolution: 3→24 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2599 1996 RANDOM
Rwork0.2292 --
all0.2599 33618 -
obs0.2599 31622 -
Refinement stepCycle: LAST / Resolution: 3→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8687 0 0 26 8713

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