[English] 日本語
Yorodumi
- PDB-5h31: Structural basis for dimerization of the death effector domains o... -

+
Open data


ID or keywords:

Loading...

-
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 / death effector domain binding / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / FasL/ CD95L signaling / TRAIL signaling / CD95 death-inducing signaling complex / ripoptosome / Defective RIPK1-mediated regulated necrosis / Apoptotic execution phase / TRAIL-activated apoptotic signaling pathway ...caspase-8 / death effector domain binding / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / FasL/ CD95L signaling / 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 / Microbial modulation of RIPK1-mediated regulated necrosis / TRIF-mediated programmed cell death / TLR3-mediated TICAM1-dependent programmed cell death / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / 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 / 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 / protein maturation / negative regulation of canonical NF-kappaB signal transduction / extrinsic apoptotic signaling pathway / cysteine-type peptidase activity / regulation of cytokine production / proteolysis involved in protein catabolic process / positive regulation of interleukin-1 beta production / T cell activation / Regulation of NF-kappa B signaling / apoptotic signaling pathway / Regulation of TNFR1 signaling / NOD1/2 Signaling Pathway / Regulation of necroptotic cell death / cellular response to mechanical stimulus / positive regulation of neuron apoptotic process / lamellipodium / response to estradiol / peptidase activity / heart development / cell body / scaffold protein binding / angiogenesis / positive regulation of canonical NF-kappaB signal transduction / response to ethanol / response to lipopolysaccharide / mitochondrial outer membrane / 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 / nucleoplasm / identical protein binding / cytosol / cytoplasm
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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,

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more