[English] 日本語
Yorodumi
- EMDB-49266: Cryo-EM structure of Fas-FADD complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49266
TitleCryo-EM structure of Fas-FADD complex
Map dataCryo-EM structure of Fas-FADD complex
Sample
  • Complex: Human Fas-FADD DD complex
    • Protein or peptide: Tumor necrosis factor receptor superfamily member 6
    • Protein or peptide: FAS-associated death domain protein
KeywordsFas / CD94 / FADD / Caspase / DISC / Apoptosis / Innate Immunity / helical assembly / IMMUNE SYSTEM
Function / homology
Function and homology information


positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / Fas signaling pathway / cellular response to hyperoxia / negative regulation of activation-induced cell death of T cells / death effector domain binding / tumor necrosis factor receptor activity / tumor necrosis factor receptor superfamily binding / FasL/ CD95L signaling / TRAIL signaling / CD95 death-inducing signaling complex ...positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / Fas signaling pathway / cellular response to hyperoxia / negative regulation of activation-induced cell death of T cells / death effector domain binding / tumor necrosis factor receptor activity / tumor necrosis factor receptor superfamily binding / FasL/ CD95L signaling / TRAIL signaling / CD95 death-inducing signaling complex / activation-induced cell death of T cells / death-inducing signaling complex assembly / ripoptosome / Defective RIPK1-mediated regulated necrosis / TRAIL-activated apoptotic signaling pathway / caspase binding / TRIF-mediated programmed cell death / 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 / receptor serine/threonine kinase binding / negative regulation of necroptotic process / positive regulation of type I interferon-mediated signaling pathway / tumor necrosis factor receptor binding / positive regulation of innate immune response / death receptor binding / positive regulation of extrinsic apoptotic signaling pathway / TP53 Regulates Transcription of Death Receptors and Ligands / TNFR1-induced proapoptotic signaling / motor neuron apoptotic process / RIPK1-mediated regulated necrosis / regulation of stress-activated MAPK cascade / positive regulation of reactive oxygen species biosynthetic process / 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 / cellular response to amino acid starvation / thymus development / positive regulation of apoptotic signaling pathway / positive regulation of interleukin-8 production / apoptotic signaling pathway / kidney development / Regulation of TNFR1 signaling / cellular response to mechanical stimulus / Regulation of necroptotic cell death / positive regulation of T cell mediated cytotoxicity / kinase binding / cytoplasmic side of plasma membrane / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / T cell differentiation in thymus / signaling receptor activity / cell body / protease binding / protein-containing complex assembly / protein-macromolecule adaptor activity / regulation of apoptotic process / defense response to virus / calmodulin binding / positive regulation of canonical NF-kappaB signal transduction / nuclear body / immune response / positive regulation of apoptotic process / membrane raft / innate immune response / external side of plasma membrane / apoptotic process / negative regulation of apoptotic process / protein-containing complex binding / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / plasma membrane / cytoplasm / cytosol
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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsFosuah E / Lin Q / Shen Z / Fu TM
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Assembly and activation of the death-inducing signaling complex
Authors: Fosuah E / Shen Z / Xie J / Wang C / Lin Q / Fu TM
History
DepositionFeb 17, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_49266.png

Downloads & links

-
Map

FileDownload / File: emd_49266.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of Fas-FADD complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 279.04 Å		1.09 Å/pix.
x 256 pix.
= 279.04 Å		1.09 Å/pix.
x 256 pix.
= 279.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.089
Minimum - Maximum-1.0982025 - 1.714298
Average (Standard dev.)-0.00039280945 (±0.027412472)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 279.04 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Additional Map

Fileemd_49266_additional_1.map
AnnotationAdditional Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map A

Fileemd_49266_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map B

Fileemd_49266_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human Fas-FADD DD complex

EntireName: Human Fas-FADD DD complex
Components
  • Complex: Human Fas-FADD DD complex
    • Protein or peptide: Tumor necrosis factor receptor superfamily member 6
    • Protein or peptide: FAS-associated death domain protein

-
Supramolecule #1: Human Fas-FADD DD complex

SupramoleculeName: Human Fas-FADD DD complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Tumor necrosis factor receptor superfamily member 6

MacromoleculeName: Tumor necrosis factor receptor superfamily member 6 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.857491 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
SDVDLSKYIT TIAGVMTLSQ VKGFVRKNGV NEAKIDEIKN DNVQDTAEQK VQLLRNWHQL HGKKEAYDTL IKDLKKANLC TLAEKIQTI ILKDITS

UniProtKB: Tumor necrosis factor receptor superfamily member 6

-
Macromolecule #2: FAS-associated death domain protein

MacromoleculeName: FAS-associated death domain protein / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.554015 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
APGEEDLCAA FNVICDNVGK DWRRLARQLK VSDTKIDSIE DRYPRNLTER VRESLRIWKN TEKENATVAH LVGALRSCQM NLVADLVQE VQQARDLQNR SG

UniProtKB: FAS-associated death domain protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 643286
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
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