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- PDB-4zbw: Crystal structure of death effector domain of Caspase8 in Homo Sapiens -

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Basic information

Entry
Database: PDB / ID: 4zbw
TitleCrystal structure of death effector domain of Caspase8 in Homo Sapiens
ComponentsCaspase-8
KeywordsHYDROLASE / Death effector domain / caspase
Function / homology
Function and homology information


caspase-8 / death effector domain binding / FasL/ CD95L signaling / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / TRAIL signaling / CD95 death-inducing signaling complex / ripoptosome / Defective RIPK1-mediated regulated necrosis / TRAIL-activated apoptotic signaling pathway / Apoptotic execution phase ...caspase-8 / death effector domain binding / FasL/ CD95L signaling / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / TRAIL signaling / CD95 death-inducing signaling complex / ripoptosome / Defective RIPK1-mediated regulated necrosis / TRAIL-activated apoptotic signaling pathway / Apoptotic execution phase / 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 / 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 / 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 / Caspase-mediated cleavage of cytoskeletal proteins / negative regulation of canonical NF-kappaB signal transduction / extrinsic apoptotic signaling pathway / 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 / protein-containing complex / mitochondrion / proteolysis / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Caspase-8 / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Death effector domain / Death Domain, Fas / Death Domain, Fas / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 ...Caspase-8 / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Death effector domain / Death Domain, Fas / Death Domain, Fas / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsShen, C. / Wang, T. / Quan, J.
Funding support China, 3items
OrganizationGrant numberCountry
MOST2012CB722602 China
MOST2013CB911501 China
SZSTIGGJS20130329180714793 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Crystal structure of the death effector domains of caspase-8
Authors: Shen, C. / Yue, H. / Pei, J. / Guo, X. / Wang, T. / Quan, J.M.
History
DepositionApr 15, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Caspase-8
B: Caspase-8


Theoretical massNumber of molelcules
Total (without water)44,9782
Polymers44,9782
Non-polymers00
Water4,468248
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint2 kcal/mol
Surface area20260 Å2
Unit cell
Length a, b, c (Å)51.360, 52.106, 56.596
Angle α, β, γ (deg.)113.34, 116.89, 90.12
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Caspase-8 / CASP-8 / Apoptotic cysteine protease / Apoptotic protease Mch-5 / CAP4 / FADD-homologous ICE/ced-3- ...CASP-8 / Apoptotic cysteine protease / Apoptotic protease Mch-5 / CAP4 / FADD-homologous ICE/ced-3-like protease / FADD-like ICE / FLICE / ICE-like apoptotic protease 5 / MORT1-associated ced-3 homolog / MACH


Mass: 22488.879 Da / Num. of mol.: 2 / Mutation: F122A, I128D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP8, MCH5 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 plysS / References: UniProt: Q14790, caspase-8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 54.26 % / Description: rod like crystal, 0.1X0.1X0.4
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.5 / Details: 0.2M sodium chloride, 25% PEG3350 / PH range: 8.0-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-002+ / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 27, 2014
RadiationMonochromator: Confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→29.22 Å / Num. obs: 22971 / % possible obs: 96.6 % / Redundancy: 1.83 % / Biso Wilson estimate: 30.98 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.59 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 2.6 / % possible all: 93.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
CrystalClear1.4data reduction
d*TREK9.7data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BBR

2bbr


Resolution: 2.2→29.22 Å / SU ML: 0.3 / Cross valid method: NONE / σ(F): 1.96 / Phase error: 28.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2010 8.76 %Random
Rwork0.2041 ---
obs0.2082 22952 96.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.3 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3050 0 0 248 3298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043082
X-RAY DIFFRACTIONf_angle_d0.84120
X-RAY DIFFRACTIONf_dihedral_angle_d14.6831248
X-RAY DIFFRACTIONf_chiral_restr0.029462
X-RAY DIFFRACTIONf_plane_restr0.005532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.34821440.28141417X-RAY DIFFRACTION92
2.255-2.3160.33521270.25561518X-RAY DIFFRACTION97
2.316-2.38410.28261610.24211500X-RAY DIFFRACTION98
2.3841-2.4610.30591400.23471544X-RAY DIFFRACTION98
2.461-2.54890.27161390.23361510X-RAY DIFFRACTION99
2.5489-2.65090.27461380.23211517X-RAY DIFFRACTION98
2.6509-2.77150.28891510.231545X-RAY DIFFRACTION98
2.7715-2.91740.30991380.24181528X-RAY DIFFRACTION98
2.9174-3.10.33521440.23441515X-RAY DIFFRACTION98
3.1-3.33910.26241440.2251550X-RAY DIFFRACTION97
3.3391-3.67450.24271580.20211461X-RAY DIFFRACTION97
3.6745-4.20490.23841520.16981469X-RAY DIFFRACTION96
4.2049-5.29260.17331480.14911459X-RAY DIFFRACTION94
5.2926-29.22470.18511260.17381409X-RAY DIFFRACTION90
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.71570.84731.43791.98371.20352.7121-0.057-0.00050.1561-0.0878-0.02490.0928-0.08560.02950.05920.24540.00970.04370.24190.01450.2876-19.535422.4626-38.9367
21.7739-0.6627-1.30491.76731.02672.0844-0.04340.0371-0.18290.1065-0.0390.120.1169-0.01980.07380.1959-0.0001-0.03820.18740.01760.2216.1586-3.2216-42.4737
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'

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