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Protein

Cell death protein 4

Gene

ced-4

Organism
Caenorhabditis elegans
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

May regulate oocyte growth. May regulate germline apoptosis in response to DNA damage, probably downstream of let-60/ras and mpk-1 pathway.1 Publication
Isoform a: Plays a major role in programmed cell death (PCD, apoptosis). Egl-1 binds to and directly inhibits the activity of ced-9, releasing the cell death activator ced-4 from a ced-9/ced-4 containing protein complex and allowing ced-4 to activate the cell-killing caspase ced-3.5 Publications
Isoform b: Prevents programmed cell death.1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi159 – 1668ATPSequence analysis

GO - Molecular functioni

  • ADP binding Source: InterPro
  • ATP binding Source: WormBase
  • BH1 domain binding Source: WormBase
  • BH3 domain binding Source: WormBase
  • cysteine-type endopeptidase activator activity involved in apoptotic process Source: GO_Central
  • endopeptidase activator activity Source: WormBase
  • peptidase activator activity involved in apoptotic process Source: WormBase

GO - Biological processi

  • activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c Source: GO_Central
  • apoptotic process Source: UniProtKB
  • apoptotic process involved in development Source: UniProtKB
  • embryo development ending in birth or egg hatching Source: WormBase
  • embryonic morphogenesis Source: WormBase
  • negative regulation of apoptotic process Source: UniProtKB
  • positive regulation of apoptotic process Source: WormBase
  • positive regulation of cysteine-type endopeptidase activity Source: WormBase
  • positive regulation of protein processing Source: WormBase
  • regulation of cell adhesion Source: UniProtKB
  • regulation of cell size Source: WormBase
  • regulation of cysteine-type endopeptidase activity involved in apoptotic process Source: WormBase
Complete GO annotation...

Keywords - Biological processi

Apoptosis

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Cell death protein 4
Gene namesi
Name:ced-4
ORF Names:C35D10.9
OrganismiCaenorhabditis elegans
Taxonomic identifieri6239 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
Proteomesi
  • UP000001940 Componenti: Chromosome III

Organism-specific databases

WormBaseiC35D10.9a; CE01203; WBGene00000418; ced-4.
C35D10.9b; CE38154; WBGene00000418; ced-4.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: UniProtKB
  • membrane Source: WormBase
  • mitochondrion Source: UniProtKB
  • nucleus Source: UniProtKB
  • perinuclear region of cytoplasm Source: WormBase
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

Pathology & Biotechi

Disruption phenotypei

Mutants exhibit a block in almost all programmed cell deaths that normally occur during development.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 571571Cell death protein 4PRO_0000089470Add
BLAST

Proteomic databases

EPDiP30429.
PaxDbiP30429.

Expressioni

Developmental stagei

Most abundant during embryogenesis and is also detected at later stages during periods of extensive programmed cell death.1 Publication

Interactioni

Subunit structurei

Interacts with ced-9.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
BCL2L1Q078172EBI-536271,EBI-78035From a different organism.
ced-3P4257310EBI-536271,EBI-494247
ced-9P4195817EBI-494118,EBI-494110

GO - Molecular functioni

  • BH1 domain binding Source: WormBase
  • BH3 domain binding Source: WormBase

Protein-protein interaction databases

BioGridi40877. 5 interactions.
DIPiDIP-1016N.
IntActiP30429. 5 interactions.
MINTiMINT-128892.
STRINGi6239.C35D10.9b.

Structurei

Secondary structure

1
571
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 2017Combined sources
Helixi23 – 264Combined sources
Helixi27 – 326Combined sources
Helixi38 – 458Combined sources
Beta strandi47 – 493Combined sources
Helixi50 – 6415Combined sources
Beta strandi66 – 683Combined sources
Helixi69 – 779Combined sources
Helixi81 – 9616Combined sources
Helixi101 – 1044Combined sources
Turni105 – 1084Combined sources
Helixi112 – 12110Combined sources
Helixi134 – 14714Combined sources
Beta strandi150 – 1589Combined sources
Helixi165 – 17511Combined sources
Turni181 – 1833Combined sources
Beta strandi184 – 1918Combined sources
Beta strandi196 – 1983Combined sources
Helixi199 – 21113Combined sources
Beta strandi239 – 2413Combined sources
Helixi250 – 26112Combined sources
Beta strandi267 – 2748Combined sources
Helixi277 – 2859Combined sources
Beta strandi289 – 2968Combined sources
Helixi297 – 3026Combined sources
Beta strandi307 – 3115Combined sources
Helixi317 – 32610Combined sources
Helixi336 – 34813Combined sources
Helixi352 – 3598Combined sources
Beta strandi364 – 3663Combined sources
Helixi367 – 38014Combined sources
Helixi381 – 3844Combined sources
Beta strandi389 – 3957Combined sources
Helixi396 – 40510Combined sources
Helixi409 – 4146Combined sources
Helixi417 – 4193Combined sources
Helixi429 – 4357Combined sources
Helixi450 – 4589Combined sources
Turni459 – 4613Combined sources
Beta strandi462 – 4643Combined sources
Beta strandi466 – 4694Combined sources
Beta strandi471 – 4733Combined sources
Beta strandi475 – 4773Combined sources
Helixi480 – 4878Combined sources
Helixi493 – 4997Combined sources
Turni503 – 5053Combined sources
Turni510 – 5123Combined sources
Helixi555 – 5584Combined sources
Helixi559 – 5624Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2A5YX-ray2.60B/C1-571[»]
3LQQX-ray3.53A/B1-571[»]
3LQRX-ray3.90A/B1-571[»]
4M9SX-ray3.21A/B/C/D1-571[»]
4M9XX-ray3.34A/B1-571[»]
4M9YX-ray4.20A/B1-571[»]
4M9ZX-ray3.40A/B/C/D1-571[»]
ProteinModelPortaliP30429.
SMRiP30429. Positions 1-571.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP30429.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 9191CARDPROSITE-ProRule annotationAdd
BLAST
Domaini116 – 440325NB-ARCAdd
BLAST

Sequence similaritiesi

Contains 1 CARD domain.PROSITE-ProRule annotation
Contains 1 NB-ARC domain.Curated

Phylogenomic databases

eggNOGiKOG4658. Eukaryota.
COG4886. LUCA.
HOGENOMiHOG000111533.
InParanoidiP30429.
KOiK20105.
OMAiAIMESYK.
OrthoDBiEOG79PJP0.
PhylomeDBiP30429.

Family and domain databases

Gene3Di1.10.533.10. 1 hit.
InterProiIPR016854. Apop_reg_Ced-4.
IPR001315. CARD.
IPR011029. DEATH-like_dom.
IPR002182. NB-ARC.
IPR027417. P-loop_NTPase.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF00619. CARD. 1 hit.
PF00931. NB-ARC. 1 hit.
[Graphical view]
PIRSFiPIRSF027202. Apop_reg_Ced-4. 1 hit.
SMARTiSM00114. CARD. 1 hit.
[Graphical view]
SUPFAMiSSF46785. SSF46785. 1 hit.
SSF47986. SSF47986. 1 hit.
SSF52540. SSF52540. 1 hit.
PROSITEiPS50209. CARD. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform b (identifier: P30429-1) [UniParc]FASTAAdd to basket

Also known as: Long

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MLCEIECRAL STAHTRLIHD FEPRDALTYL EGKNIFTEDH SELISKMSTR
60 70 80 90 100
LERIANFLRI YRRQASELGP LIDFFNYNNQ SHLADFLEDY IDFAINEPDL
110 120 130 140 150
LRPVVIAPQF SRQMLDRKLL LGNVPKQMTC YIREYHVDRV IKKLDEMCDL
160 170 180 190 200
DSFFLFLHGR AGSGKSVIAS QALSKSDQLI GINYDSIVWL KDSGTAPKST
210 220 230 240 250
FDLFTDILLM LARVVSDTDD SHSITDFINR VLSRSEDDLL NFPSVEHVTS
260 270 280 290 300
VVLKRMICNA LIDRPNTLFV FDDVVQEETI RWAQELRLRC LVTTRDVEIS
310 320 330 340 350
NAASQTCEFI EVTSLEIDEC YDFLEAYGMP MPVGEKEEDV LNKTIELSSG
360 370 380 390 400
NPATLMMFFK SCEPKTFEKM AQLNNKLESR GLVGVECITP YSYKSLAMAL
410 420 430 440 450
QRCVEVLSDE DRSALAFAVV MPPGVDIPVK LWSCVIPVDI CSNEEEQLDD
460 470 480 490 500
EVADRLKRLS KRGALLSGKR MPVLTFKIDH IIHMFLKHVV DAQTIANGIS
510 520 530 540 550
ILEQRLLEIG NNNVSVPERH IPSHFQKFRR SSASEMYPKT TEETVIRPED
560 570
FPKFMQLHQK FYDSLKNFAC C
Note: Minor transcript.
Length:571
Mass (Da):65,336
Last modified:March 29, 2005 - v2
Checksum:i6BE9893946B79E6C
GO
Isoform a (identifier: P30429-2) [UniParc]FASTAAdd to basket

Also known as: Short

The sequence of this isoform differs from the canonical sequence as follows:
     212-234: ARVVSDTDDSHSITDFINRVLSR → K

Note: Major transcript.
Show »
Length:549
Mass (Da):62,878
Checksum:iDB2A7969BDA50AF8
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei212 – 23423ARVVS…RVLSR → K in isoform a. CuratedVSP_013199Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X69016 Genomic DNA. Translation: CAA48781.1.
FO080789 Genomic DNA. Translation: CCD66781.1.
FO080789 Genomic DNA. Translation: CCD66782.1.
PIRiS72566.
RefSeqiNP_001021202.1. NM_001026031.2. [P30429-2]
NP_001021203.1. NM_001026032.1. [P30429-1]
UniGeneiCel.10679.

Genome annotation databases

EnsemblMetazoaiC35D10.9b; C35D10.9b; WBGene00000418. [P30429-1]
GeneIDi175643.
KEGGicel:CELE_C35D10.9.
UCSCiC35D10.9b. c. elegans. [P30429-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X69016 Genomic DNA. Translation: CAA48781.1.
FO080789 Genomic DNA. Translation: CCD66781.1.
FO080789 Genomic DNA. Translation: CCD66782.1.
PIRiS72566.
RefSeqiNP_001021202.1. NM_001026031.2. [P30429-2]
NP_001021203.1. NM_001026032.1. [P30429-1]
UniGeneiCel.10679.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2A5YX-ray2.60B/C1-571[»]
3LQQX-ray3.53A/B1-571[»]
3LQRX-ray3.90A/B1-571[»]
4M9SX-ray3.21A/B/C/D1-571[»]
4M9XX-ray3.34A/B1-571[»]
4M9YX-ray4.20A/B1-571[»]
4M9ZX-ray3.40A/B/C/D1-571[»]
ProteinModelPortaliP30429.
SMRiP30429. Positions 1-571.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi40877. 5 interactions.
DIPiDIP-1016N.
IntActiP30429. 5 interactions.
MINTiMINT-128892.
STRINGi6239.C35D10.9b.

Proteomic databases

EPDiP30429.
PaxDbiP30429.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiC35D10.9b; C35D10.9b; WBGene00000418. [P30429-1]
GeneIDi175643.
KEGGicel:CELE_C35D10.9.
UCSCiC35D10.9b. c. elegans. [P30429-1]

Organism-specific databases

CTDi175643.
WormBaseiC35D10.9a; CE01203; WBGene00000418; ced-4.
C35D10.9b; CE38154; WBGene00000418; ced-4.

Phylogenomic databases

eggNOGiKOG4658. Eukaryota.
COG4886. LUCA.
HOGENOMiHOG000111533.
InParanoidiP30429.
KOiK20105.
OMAiAIMESYK.
OrthoDBiEOG79PJP0.
PhylomeDBiP30429.

Miscellaneous databases

EvolutionaryTraceiP30429.
PROiP30429.

Family and domain databases

Gene3Di1.10.533.10. 1 hit.
InterProiIPR016854. Apop_reg_Ced-4.
IPR001315. CARD.
IPR011029. DEATH-like_dom.
IPR002182. NB-ARC.
IPR027417. P-loop_NTPase.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF00619. CARD. 1 hit.
PF00931. NB-ARC. 1 hit.
[Graphical view]
PIRSFiPIRSF027202. Apop_reg_Ced-4. 1 hit.
SMARTiSM00114. CARD. 1 hit.
[Graphical view]
SUPFAMiSSF46785. SSF46785. 1 hit.
SSF47986. SSF47986. 1 hit.
SSF52540. SSF52540. 1 hit.
PROSITEiPS50209. CARD. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The Caenorhabditis elegans cell death gene ced-4 encodes a novel protein and is expressed during the period of extensive programmed cell death."
    Yuan J., Horvitz H.R.
    Development 116:309-320(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM A), FUNCTION, DEVELOPMENTAL STAGE, DISRUPTION PHENOTYPE.
  2. "Genome sequence of the nematode C. elegans: a platform for investigating biology."
    The C. elegans sequencing consortium
    Science 282:2012-2018(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Bristol N2.
  3. "An alternatively spliced C. elegans ced-4 RNA encodes a novel cell death inhibitor."
    Shaham S., Horvitz H.R.
    Cell 86:201-208(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ALTERNATIVE SPLICING.
  4. "Interaction and regulation of subcellular localization of CED-4 by CED-9."
    Wu D., Wallen H.D., Nunez G.
    Science 275:1126-1129(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH CED-9.
  5. "Translocation of C. elegans CED-4 to nuclear membranes during programmed cell death."
    Chen F., Hersh B.M., Conradt B., Zhou Z., Riemer D., Gruenbaum Y., Horvitz H.R.
    Science 287:1485-1489(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.
  6. "Structural, biochemical, and functional analyses of CED-9 recognition by the proapoptotic proteins EGL-1 and CED-4."
    Yan N., Gu L., Kokel D., Chai J., Li W., Han A., Chen L., Xue D., Shi Y.
    Mol. Cell 15:999-1006(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH CED-9.
  7. "Regulation of Caenorhabditis elegans p53/CEP-1-dependent germ cell apoptosis by Ras/MAPK signaling."
    Rutkowski R., Dickinson R., Stewart G., Craig A., Schimpl M., Keyse S.M., Gartner A.
    PLoS Genet. 7:E1002238-E1002238(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiCED4_CAEEL
AccessioniPrimary (citable) accession number: P30429
Secondary accession number(s): Q5BHI5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1993
Last sequence update: March 29, 2005
Last modified: July 6, 2016
This is version 137 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programCaenorhabditis annotation project

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Caenorhabditis elegans
    Caenorhabditis elegans: entries, gene names and cross-references to WormBase
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.