[English] 日本語
Yorodumi
- PDB-1fad: DEATH DOMAIN OF FAS-ASSOCIATED DEATH DOMAIN PROTEIN, RESIDUES 89-183 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fad
TitleDEATH DOMAIN OF FAS-ASSOCIATED DEATH DOMAIN PROTEIN, RESIDUES 89-183
ComponentsPROTEIN (FADD PROTEIN)
KeywordsAPOPTOSIS / FADD / DEATH DOMAIN
Function / homology
Function and homology information


positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / TRAIL signaling / FasL/ CD95L signaling / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / negative regulation of activation-induced cell death of T cells / TNFR1-induced proapoptotic signaling / Caspase activation via Death Receptors in the presence of ligand / TRIF-mediated programmed cell death ...positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / TRAIL signaling / FasL/ CD95L signaling / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / negative regulation of activation-induced cell death of T cells / TNFR1-induced proapoptotic signaling / Caspase activation via Death Receptors in the presence of ligand / TRIF-mediated programmed cell death / death effector domain binding / Regulation of TNFR1 signaling / Regulation of necroptotic cell death / CD95 death-inducing signaling complex / death-inducing signaling complex assembly / ripoptosome / TRAIL-activated apoptotic signaling pathway / caspase binding / positive regulation of adaptive immune response / positive regulation of macrophage differentiation / necroptotic signaling pathway / receptor serine/threonine kinase binding / negative regulation of necroptotic process / positive regulation of type I interferon-mediated signaling pathway / tumor necrosis factor receptor binding / death receptor binding / positive regulation of extrinsic apoptotic signaling pathway / cardiac muscle tissue development / motor neuron apoptotic process / positive regulation of activated T cell proliferation / T cell homeostasis / behavioral response to cocaine / positive regulation of proteolysis / positive regulation of execution phase of apoptosis / T cell differentiation / extrinsic apoptotic signaling pathway via death domain receptors / lymph node development / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / extrinsic apoptotic signaling pathway / signaling adaptor activity / thymus development / kidney development / positive regulation of interleukin-8 production / positive regulation of T cell mediated cytotoxicity / positive regulation of type II interferon production / cellular response to mechanical stimulus / positive regulation of tumor necrosis factor production / T cell differentiation in thymus / cell body / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / innate immune response / apoptotic process / protein-containing complex binding / positive regulation of transcription by RNA polymerase II / identical protein binding
Similarity search - Function
FADD / : / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Death effector domain / Death Domain, Fas / Death Domain, Fas / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). ...FADD / : / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Death effector domain / Death Domain, Fas / Death Domain, Fas / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FAS-associated death domain protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMMULATED ANNEALING
AuthorsJeong, E.-J. / Bang, S. / Lee, T.H. / Park, Y.-I. / Sim, W.-S. / Kim, K.-S.
Citation
Journal: J.Biol.Chem. / Year: 1999
Title: The solution structure of FADD death domain. Structural basis of death domain interactions of Fas and FADD.
Authors: Jeong, E.J. / Bang, S. / Lee, T.H. / Park, Y.I. / Sim, W.S. / Kim, K.S.
#1: Journal: Mol.Cell.Biol. / Year: 1996
Title: A Mouse Fas-Associated Protein with Homology to the Human Mort1/FADD is Essential for Fas-Induced Apoptosis
Authors: Zhang, J. / Winoto, A.
History
DepositionMar 23, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (FADD PROTEIN)


Theoretical massNumber of molelcules
Total (without water)11,0891
Polymers11,0891
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 50LOWEST ENERGY
RepresentativeModel #21

-
Components

#1: Protein PROTEIN (FADD PROTEIN)


Mass: 11088.693 Da / Num. of mol.: 1 / Fragment: DEATH DOMAIN (RESIDUES 89-183) / Mutation: D96Y
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL EXTENSION OF GLY-SER-HIS-MET FROM CLONING ARTIFACT. COORDINATES ARE NOT SHOWN FOR ARTIFACT.
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET15B / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q61160

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D-15N-HSQC-NOESY
1213D-13C
13115N-EDITED NOESY
14113C-(H)CCH-TOCSY
1513D-15N-HSQC-TOCSY
161NOESY
1713D HNHA
NMR detailsText: DISTANCE CONSTRAINTS ARE DERIVED FROM THE 3D-13C, 15N-EDITED NOESY. J-COUPLING CONSTANTS FROM HNHA AND 13C CHEMICAL SHIFTS WERE USED AS CONTRAINTS. DURING THE REFINEMENT, DATABASE POTENTIAL WAS USED.

-
Sample preparation

DetailsContents: 2 MM
Sample conditionspH: 4 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUS600VarianUNITYPLUS6005001
Varian INOVA500VarianINOVA5006002

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 21

+
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