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- PDB-1i4e: CRYSTAL STRUCTURE OF THE CASPASE-8/P35 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1i4e
TitleCRYSTAL STRUCTURE OF THE CASPASE-8/P35 COMPLEX
Components
  • Caspase-8
  • Early 35 kDa protein
KeywordsAPOPTOSIS/HYDROLASE / covalent complex protease-inhibitor / 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
AuthorsXu, G. / Cirilli, M. / Huang, Y. / Rich, R.L. / Myszka, D.G. / Wu, H.
CitationJournal: Nature / Year: 2001
Title: Covalent inhibition revealed by the crystal structure of the caspase-8/p35 complex.
Authors: Xu, G. / Cirilli, M. / Huang, Y. / Rich, R.L. / Myszka, D.G. / Wu, H.
History
DepositionFeb 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 25, 2013Group: Derived calculations
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)64,2912
Polymers64,2912
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-10 kcal/mol
Surface area26420 Å2
MethodPISA
2
A: Early 35 kDa protein
B: Caspase-8

A: Early 35 kDa protein
B: Caspase-8


Theoretical massNumber of molelcules
Total (without water)128,5824
Polymers128,5824
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area8750 Å2
ΔGint-43 kcal/mol
Surface area48420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.97, 117.34, 346.45
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 34768.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica nucleopolyhedrovirus
Genus: Escherichia / Gene: P35 / Production host: Escherichia coli (E. coli) / References: UniProt: P08160
#2: Protein Caspase-8 / CASP-8 / ICE-like apoptotic protease 5 / MORT1-associated ced-3 homolog / MACH / FADD-homologous ...CASP-8 / ICE-like apoptotic protease 5 / MORT1-associated ced-3 homolog / MACH / FADD-homologous ICE/ced-3-like protease / FADD-like ICE / FLICE / Apoptotic cysteine protease / Apoptotic protease Mch-5 / CAP4 / Caspase-8 subunit p18 / Caspase-8 subunit p10


Mass: 29522.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Genus: Escherichia / Gene: CASP8, MCH5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14790, caspase-8
Has protein modificationY
Sequence detailsD -> H AT RESIDUE 2285 OF CHAIN B IS A NATURAL VARIANT

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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

Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120-30 mg/mlprotein1drop
220 mMTris-HCl1drop
3150 mM1dropNaCl
45 mMdithiothreitol1drop
52 %PEG80001reservoir
6100 mMMOPS1reservoir
71 %2-propanol1reservoir

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Data collection

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→29.83 Å / Num. obs: 37662 / % possible obs: 91.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 18.3

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Processing

Software
NameVersionClassification
GLRFphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→24 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2957 1512 -RANDOM
Rwork0.2361 ---
obs-37649 99.1 %-
Refinement stepCycle: LAST / Resolution: 3→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4354 0 0 0 4354
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007403
X-RAY DIFFRACTIONc_angle_deg1.33107
X-RAY DIFFRACTIONc_dihedral_angle_d24.48266
X-RAY DIFFRACTIONc_improper_angle_d0.8478
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.48266
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8478

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