[English] 日本語
Yorodumi
- PDB-3oq9: Structure of the FAS/FADD death domain assembly -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3oq9
TitleStructure of the FAS/FADD death domain assembly
Components
  • Protein FADD
  • Tumor necrosis factor receptor superfamily member 6
KeywordsAPOPTOSIS / DISC / FAS / FADD
Function / homology
Function and homology information


FasL/ CD95L signaling / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / inflammatory cell apoptotic process / positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / regulation of myeloid cell differentiation / negative regulation of activation-induced cell death of T cells / negative regulation of B cell activation / regulation of B cell differentiation ...FasL/ CD95L signaling / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / inflammatory cell apoptotic process / positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / regulation of myeloid cell differentiation / negative regulation of activation-induced cell death of T cells / negative regulation of B cell activation / regulation of B cell differentiation / death effector domain binding / tumor necrosis factor receptor superfamily binding / FasL/ CD95L signaling / B cell mediated immunity / TRAIL signaling / CD95 death-inducing signaling complex / lymphocyte apoptotic process / death-inducing signaling complex assembly / activation-induced cell death of T cells / ripoptosome / Defective RIPK1-mediated regulated necrosis / TRAIL-activated apoptotic signaling pathway / TRIF-mediated programmed cell death / caspase binding / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TLR3-mediated TICAM1-dependent programmed cell death / regulation of hematopoietic progenitor cell differentiation / positive regulation of adaptive immune response / Caspase activation via Death Receptors in the presence of ligand / positive regulation of macrophage differentiation / negative thymic T cell selection / necroptotic signaling pathway / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / death-inducing signaling complex / negative regulation of necroptotic process / receptor serine/threonine kinase binding / positive regulation of type I interferon-mediated signaling pathway / tumor necrosis factor receptor binding / death receptor binding / positive regulation of innate immune response / positive regulation of extrinsic apoptotic signaling pathway / TNFR1-induced proapoptotic signaling / motor neuron apoptotic process / RIPK1-mediated regulated necrosis / regulation of T cell differentiation / cellular response to lithium ion / hepatocyte apoptotic process / positive regulation of release of cytochrome c from mitochondria / positive regulation of activated T cell proliferation / T cell homeostasis / positive regulation of proteolysis / positive regulation of execution phase of apoptosis / extrinsic apoptotic signaling pathway via death domain receptors / lymph node development / response to glucocorticoid / behavioral response to cocaine / spleen development / extrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / signaling adaptor activity / thymus development / positive regulation of interleukin-8 production / positive regulation of protein-containing complex assembly / kidney development / apoptotic signaling pathway / Regulation of TNFR1 signaling / positive regulation of T cell mediated cytotoxicity / Regulation of necroptotic cell death / response to toxic substance / cytoplasmic side of plasma membrane / cellular response to mechanical stimulus / circadian rhythm / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / transmembrane signaling receptor activity / T cell differentiation in thymus / cell body / protease binding / protein-macromolecule adaptor activity / neuron apoptotic process / defense response to virus / gene expression / positive regulation of canonical NF-kappaB signal transduction / calmodulin binding / positive regulation of apoptotic process / membrane raft / external side of plasma membrane / innate immune response / apoptotic process / negative regulation of apoptotic process / protein-containing complex binding / cell surface / positive regulation of transcription by RNA polymerase II / extracellular region / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Fas receptor / Fas receptor, death domain / Fas receptor, N-terminal / FADD / : / Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / TNFR/NGFR family cysteine-rich region domain profile. ...Fas receptor / Fas receptor, death domain / Fas receptor, N-terminal / FADD / : / Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 6 / FAS-associated death domain protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 6.8 Å
AuthorsKabaleeswaran, V. / Wu, H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: The Fas-FADD death domain complex structure reveals the basis of DISC assembly and disease mutations.
Authors: Wang, L. / Yang, J.K. / Kabaleeswaran, V. / Rice, A.J. / Cruz, A.C. / Park, A.Y. / Yin, Q. / Damko, E. / Jang, S.B. / Raunser, S. / Robinson, C.V. / Siegel, R.M. / Walz, T. / Wu, H.
History
DepositionSep 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tumor necrosis factor receptor superfamily member 6
B: Tumor necrosis factor receptor superfamily member 6
C: Tumor necrosis factor receptor superfamily member 6
D: Tumor necrosis factor receptor superfamily member 6
E: Tumor necrosis factor receptor superfamily member 6
H: Protein FADD
I: Protein FADD
J: Protein FADD
K: Protein FADD
L: Protein FADD


Theoretical massNumber of molelcules
Total (without water)109,23910
Polymers109,23910
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.204, 144.447, 131.574
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein
Tumor necrosis factor receptor superfamily member 6 / FASLG receptor / Apoptosis-mediating surface antigen FAS / Apo-1 antigen


Mass: 10162.680 Da / Num. of mol.: 5 / Fragment: UNP residues 223-308
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fas, Apt1, Tnfrsf6 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P25446
#2: Protein
Protein FADD / FAS-associated death domain protein / FAS-associating death domain-containing protein / Mediator of ...FAS-associated death domain protein / FAS-associating death domain-containing protein / Mediator of receptor induced toxicity / Growth-inhibiting gene 3 protein


Mass: 11685.176 Da / Num. of mol.: 5 / Fragment: UNP residues 93-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FADD, MORT1, GIG3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13158

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 100 mM MgCl2, 5 % glycerol and 6-10 % PEG4000, hanging drop, temperature 298K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorDetector: CCD / Date: Apr 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 6.8→50 Å / Num. obs: 2175 / % possible obs: 92.6 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.07 / Χ2: 1.649 / Net I/σ(I): 15
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
6.8-7.042.70.4621580.78369.3
7.04-7.323.20.2731890.80187.9
7.32-7.664.30.2812300.96997
7.66-8.065.20.1792231.05297.4
8.06-8.565.50.1232241.18997
8.56-9.225.70.1122221.38495.7
9.22-10.145.80.0782251.70894.9
10.14-11.595.50.062252.13997
11.59-14.545.30.0532312.34894.7
14.54-504.40.0452483.02793.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 45.091 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.52 Å49.36 Å
Translation6.52 Å49.36 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
CNSrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 6.8→20 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3542 96 4.2 %random
Rwork0.3434 ---
obs-1941 85.6 %-
Solvent computationBsol: 383.707 Å2
Displacement parametersBiso max: 452.47 Å2 / Biso mean: 452.47 Å2 / Biso min: 452.47 Å2
Baniso -1Baniso -2Baniso -3
1--86.524 Å20 Å20 Å2
2--102.559 Å20 Å2
3----16.036 Å2
Refinement stepCycle: LAST / Resolution: 6.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7255 0 0 0 7255
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_d1.722
Xplor fileSerial no: 1 / Param file: CNS_TOPPAR:protein_rep.param

+
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