[English] 日本語
Yorodumi
- PDB-9u7a: FADD-DED filaments coordinate complex IIa assembly during TNF-ind... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9u7a
TitleFADD-DED filaments coordinate complex IIa assembly during TNF-induced apoptosis
ComponentsFAS-associated death domain protein
KeywordsIMMUNE SYSTEM / RNA recognition / RNA helicase / ATP hydrolysis / RLR signaling
Function / homology
Function and homology information


positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / negative regulation of activation-induced cell death of T cells / death effector domain binding / tumor necrosis factor receptor superfamily binding / FasL/ CD95L signaling / TRAIL signaling / CD95 death-inducing signaling complex / death-inducing signaling complex assembly / ripoptosome / Defective RIPK1-mediated regulated necrosis ...positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / negative regulation of activation-induced cell death of T cells / death effector domain binding / tumor necrosis factor receptor superfamily binding / FasL/ CD95L signaling / TRAIL signaling / CD95 death-inducing signaling complex / death-inducing signaling complex assembly / 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 / positive regulation of adaptive immune response / Caspase activation via Death Receptors in the presence of ligand / positive regulation of macrophage differentiation / 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 / positive regulation of activated T cell proliferation / T cell homeostasis / positive regulation of proteolysis / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of execution phase of apoptosis / lymph node development / behavioral response to cocaine / spleen development / extrinsic apoptotic signaling pathway / signaling adaptor activity / extrinsic apoptotic signaling pathway in absence of ligand / thymus development / Regulation of TNFR1 signaling / positive regulation of interleukin-8 production / apoptotic signaling pathway / kidney development / Regulation of necroptotic cell death / cellular response to mechanical stimulus / positive regulation of T cell mediated cytotoxicity / cytoplasmic side of plasma membrane / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / T cell differentiation in thymus / cell body / protease binding / protein-macromolecule adaptor activity / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / positive regulation of apoptotic process / innate immune response / apoptotic process / protein-containing complex binding / positive regulation of transcription by RNA polymerase II / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
FADD / : / Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / 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
FAS-associated death domain protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsLiu, P. / Luo, D.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF-CRP26-2021-0001 Singapore
CitationJournal: To Be Published
Title: FADD-DED filaments coordinate complex IIa assembly during TNF-induced apoptosis
Authors: Liu, P. / Luo, D.
History
DepositionMar 24, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: FAS-associated death domain protein
C: FAS-associated death domain protein
D: FAS-associated death domain protein
E: FAS-associated death domain protein
F: FAS-associated death domain protein
G: FAS-associated death domain protein
H: FAS-associated death domain protein
I: FAS-associated death domain protein
J: FAS-associated death domain protein
K: FAS-associated death domain protein
L: FAS-associated death domain protein
M: FAS-associated death domain protein
N: FAS-associated death domain protein
O: FAS-associated death domain protein
P: FAS-associated death domain protein
Q: FAS-associated death domain protein
R: FAS-associated death domain protein
S: FAS-associated death domain protein
T: FAS-associated death domain protein
U: FAS-associated death domain protein
V: FAS-associated death domain protein
W: FAS-associated death domain protein
X: FAS-associated death domain protein
Y: FAS-associated death domain protein


Theoretical massNumber of molelcules
Total (without water)244,84124
Polymers244,84124
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein ...
FAS-associated death domain protein / FAS-associating death domain-containing protein / Growth-inhibiting gene 3 protein / Mediator of ...FAS-associating death domain-containing protein / Growth-inhibiting gene 3 protein / Mediator of receptor induced toxicity


Mass: 10201.722 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FADD, MORT1, GIG3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13158
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1FADD-DED filamentCOMPLEXFADD-DED filament formation during apoptosisall0RECOMBINANT
2FADD-filamentCOMPLEXFADD-filamentall1RECOMBINANT
Molecular weightValue: 0.42 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5 / Details: 25mM HEPES, 150mM NaCl
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESHEPES1
2150 mMsodium chlorideNaCl1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The sample forms filament.
Specimen supportGrid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6163

-
Processing

EM software
IDNameVersionCategoryDetails
1Topazparticle selection
2cryoSPARCparticle selection
3EPUimage acquisition
5cryoSPARCCTF correction
8UCSF ChimeraXmodel fitting
10PHENIX1.20.1_4487:model refinement
11Cootmodel refinement
12cryoSPARCinitial Euler assignment
13cryoSPARCfinal Euler assignmenthelical refinement
14cryoSPARCclassificationheterogenous refinement
15cryoSPARC3D reconstructionhelical refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionDetails: topaz train/extract
3D reconstructionResolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90187 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingDetails: ModelAngelo / Source name: Other / Type: in silico model

+
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