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- PDB-5h31: Structural basis for dimerization of the death effector domains o... -

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Basic information

Entry
Database: PDB / ID: 5h31
TitleStructural basis for dimerization of the death effector domains of Caspase-8
ComponentsCaspase-8
KeywordsHYDROLASE / DEATH EFFECTOR DOMAIN / CASPASE
Function / homology
Function and homology information


caspase-8 / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / death effector domain binding / FasL/ CD95L signaling / TRAIL signaling / CD95 death-inducing signaling complex / Apoptotic execution phase / Activation, myristolyation of BID and translocation to mitochondria / ripoptosome / Defective RIPK1-mediated regulated necrosis ...caspase-8 / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / death effector domain binding / FasL/ CD95L signaling / TRAIL signaling / CD95 death-inducing signaling complex / Apoptotic execution phase / Activation, myristolyation of BID and translocation to mitochondria / ripoptosome / Defective RIPK1-mediated regulated necrosis / Microbial modulation of RIPK1-mediated regulated necrosis / TRAIL-activated apoptotic signaling pathway / TRIF-mediated programmed cell death / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TLR3-mediated TICAM1-dependent programmed cell death / self proteolysis / Caspase activation via Death Receptors in the presence of ligand / positive regulation of macrophage differentiation / response to cobalt ion / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / CLEC7A/inflammasome pathway / death-inducing signaling complex / negative regulation of necroptotic process / 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 / response to anesthetic / execution phase of apoptosis / regulation of innate immune response / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / response to tumor necrosis factor / B cell activation / positive regulation of proteolysis / macrophage differentiation / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of execution phase of apoptosis / 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 / proteolysis involved in protein catabolic process / T cell activation / protein maturation / positive regulation of interleukin-1 beta production / Regulation of NF-kappa B signaling / apoptotic signaling pathway / Regulation of TNFR1 signaling / cellular response to mechanical stimulus / NOD1/2 Signaling Pathway / protein processing / Regulation of necroptotic cell death / response to estradiol / peptidase activity / positive regulation of neuron apoptotic process / lamellipodium / heart development / cell body / scaffold protein binding / response to ethanol / angiogenesis / response to lipopolysaccharide / mitochondrial outer membrane / cytoskeleton / positive regulation of canonical NF-kappaB signal transduction / 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 / cytoplasm / cytosol
Similarity search - Function
Caspase-8 / Death effector domain / Death effector domain / Death effector domain (DED) profile. / 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 / Death effector domain (DED) profile. / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.16953525699 Å
AuthorsShen, C. / Pei, J. / Guo, X. / Quan, J.
Citation
Journal: To Be Published
Title: Structural basis for dimerization of the death effector domains of Caspase-8
Authors: Shen, C. / Pei, J. / Guo, X. / Zhou, L. / Li, Q. / Quan, J.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution
Authors: Adams, P.D. / Afonine, P.V. / Bunkoczi, G. / Chen, V.B. / Davis, I.W. / Echols, N. / Headd, J.J. / Kapral, G.J. / Hung, L.W. / McCoy, A.J. / Grosse-Kunstleve, R.W. / Moriarty, N.W. / ...Authors: Adams, P.D. / Afonine, P.V. / Bunkoczi, G. / Chen, V.B. / Davis, I.W. / Echols, N. / Headd, J.J. / Kapral, G.J. / Hung, L.W. / McCoy, A.J. / Grosse-Kunstleve, R.W. / Moriarty, N.W. / Oeffner, R. / Read, R.J. / Richardson, D.C. / Richardson, J.S. / Quan, J. / Shen, C.
#3: Journal: Biochem. Biophys. Res. Commun. / Year: 2015
Title: Crystal structure of the death effector domains of caspase-8
Authors: Terwilliger, T.C. / Zwart, P.H.
History
DepositionOct 19, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)89,3714
Polymers89,3714
Non-polymers00
Water00
1
A: Caspase-8
B: Caspase-8


Theoretical massNumber of molelcules
Total (without water)44,6862
Polymers44,6862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-57 kcal/mol
Surface area20390 Å2
MethodPISA
2
C: Caspase-8
D: Caspase-8


Theoretical massNumber of molelcules
Total (without water)44,6862
Polymers44,6862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-59 kcal/mol
Surface area20330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.774, 51.706, 171.959
Angle α, β, γ (deg.)90.0, 90.054, 90.0
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 2 - 183 / Label seq-ID: 2 - 183

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11chain 'A'AA
22chain 'B'BB
33chain 'C'CC
44chain 'D'DD

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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: 22342.820 Da / Num. of mol.: 4 / Fragment: UNP residues 1-188 / Mutation: F122A
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

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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: 2.66 Å3/Da / Density % sol: 53.69 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.5
Details: 100 mM sodium chloride, 100 mM Tris, 21% PEG3350, 10 mM Sarcosine,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9779 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 15236 / % possible obs: 99.7 % / Redundancy: 11.5 % / Biso Wilson estimate: 75.6376901329 Å2 / Net I/σ(I): 12.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.16953525699→49.588572546 Å / SU ML: 0.433232462914 / Cross valid method: THROUGHOUT / σ(F): 1.33645866753 / Phase error: 30.4688474617
RfactorNum. reflection% reflection
Rfree0.268227785858 1525 10.0091887635 %
Rwork0.224713135643 --
obs0.228976096656 15236 96.1443806399 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 73.1670414201 Å2
Refinement stepCycle: LAST / Resolution: 3.16953525699→49.588572546 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6064 0 0 0 6064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001739029724346128
X-RAY DIFFRACTIONf_angle_d0.4746777920478192
X-RAY DIFFRACTIONf_chiral_restr0.0171123730476924
X-RAY DIFFRACTIONf_plane_restr0.003639640187731052
X-RAY DIFFRACTIONf_dihedral_angle_d13.03406118412480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1695-3.27180.3674374712311220.310833555481113X-RAY DIFFRACTION86.3636363636
3.2718-3.38870.3767131969971410.3026947701571230X-RAY DIFFRACTION95.9412176347
3.3887-3.52440.3225482826441350.3007075494371229X-RAY DIFFRACTION95.7865168539
3.5244-3.68470.3683184931881440.2558294639581215X-RAY DIFFRACTION95.9068454481
3.6847-3.87890.2728420064671280.2620926208951237X-RAY DIFFRACTION96.8085106383
3.8789-4.12180.3230395314581360.2339400035171240X-RAY DIFFRACTION96.3585434174
4.1218-4.43990.2727984141361450.2018803821821265X-RAY DIFFRACTION96.70781893
4.4399-4.88640.2832652767061350.2005876428531240X-RAY DIFFRACTION96.8309859155
4.8864-5.59260.260351723671360.2183566347141293X-RAY DIFFRACTION98.4838042729
5.5926-7.04290.2149135602881470.2408241078761291X-RAY DIFFRACTION99.0358126722
7.0429-49.59460.1896687191591560.1708513583381358X-RAY DIFFRACTION99.2136304063

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