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Protein

Programmed cell death protein 10

Gene

PDCD10

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Promotes cell proliferation. Modulates apoptotic pathways. Increases mitogen-activated protein kinase activity and STK26 activity (PubMed:27807006). Important for cell migration, and for normal structure and assembly of the Golgi complex (PubMed:27807006). Important for KDR/VEGFR2 signaling. Increases the stability of KDR/VEGFR2 and prevents its breakdown. Required for normal cardiovascular development. Required for normal angiogenesis, vasculogenesis and hematopoiesis during embryonic development (By similarity).By similarity4 Publications

GO - Molecular functioni

  • protein homodimerization activity Source: UniProtKB
  • protein kinase binding Source: UniProtKB
  • protein N-terminus binding Source: UniProtKB

GO - Biological processi

  • angiogenesis Source: UniProtKB-KW
  • cellular response to leukemia inhibitory factor Source: Ensembl
  • establishment of Golgi localization Source: UniProtKB
  • Golgi reassembly Source: UniProtKB
  • intrinsic apoptotic signaling pathway in response to hydrogen peroxide Source: UniProtKB
  • negative regulation of apoptotic process Source: UniProtKB
  • negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis Source: UniProtKB
  • negative regulation of cell migration involved in sprouting angiogenesis Source: UniProtKB
  • negative regulation of gene expression Source: UniProtKB
  • positive regulation of cell migration Source: UniProtKB
  • positive regulation of cell proliferation Source: UniProtKB
  • positive regulation of gene expression Source: UniProtKB
  • positive regulation of intracellular protein transport Source: UniProtKB
  • positive regulation of MAP kinase activity Source: UniProtKB
  • positive regulation of Notch signaling pathway Source: UniProtKB
  • positive regulation of peptidyl-serine phosphorylation Source: UniProtKB
  • positive regulation of protein serine/threonine kinase activity Source: UniProtKB
  • positive regulation of stress-activated MAPK cascade Source: UniProtKB
  • protein stabilization Source: UniProtKB
  • response to hydrogen peroxide Source: UniProtKB
  • wound healing, spreading of cells Source: UniProtKB

Keywordsi

Biological processAngiogenesis, Apoptosis

Enzyme and pathway databases

SIGNORiQ9BUL8

Names & Taxonomyi

Protein namesi
Recommended name:
Programmed cell death protein 10
Alternative name(s):
Cerebral cavernous malformations 3 protein
TF-1 cell apoptosis-related protein 15
Gene namesi
Name:PDCD10
Synonyms:CCM3, TFAR15
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 3

Organism-specific databases

EuPathDBiHostDB:ENSG00000114209.14
HGNCiHGNC:8761 PDCD10
MIMi609118 gene
neXtProtiNX_Q9BUL8

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cell membrane, Cytoplasm, Golgi apparatus, Membrane

Pathology & Biotechi

Involvement in diseasei

Cerebral cavernous malformations 3 (CCM3)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA congenital vascular anomaly of the central nervous system that can result in hemorrhagic stroke, seizures, recurrent headaches, and focal neurologic deficits. The lesions are characterized by grossly enlarged blood vessels consisting of a single layer of endothelium and without any intervening neural tissue, ranging in diameter from a few millimeters to several centimeters.
See also OMIM:603285

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi132K → D: Loss of interaction with CCM2 and PXN; when associated with D-139; D-172 and D-179. 1 Publication1
Mutagenesisi135A → D: Loss of interaction with CCM2. 1 Publication1
Mutagenesisi139K → D: Loss of interaction with CCM2 and PXN; when associated with D-132; D-172 and D-179. 1 Publication1
Mutagenesisi172K → D: Loss of interaction with CCM2 and PXN; when associated with D-132; D-139 and D-179. 1 Publication1
Mutagenesisi175S → D: Loss of interaction with CCM2. 1 Publication1
Mutagenesisi179K → D: Loss of interaction with CCM2 and PXN; when associated with D-132; D-139 and D-172. 1 Publication1

Organism-specific databases

DisGeNETi11235
GeneReviewsiPDCD10
MalaCardsiPDCD10
MIMi603285 phenotype
OpenTargetsiENSG00000114209
Orphaneti221061 Hereditary cerebral cavernous malformation
PharmGKBiPA33111

Polymorphism and mutation databases

BioMutaiPDCD10
DMDMi74733232

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001875621 – 212Programmed cell death protein 10Add BLAST212

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei179N6-acetyllysineCombined sources1
Cross-linki186Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources

Keywords - PTMi

Acetylation, Isopeptide bond, Ubl conjugation

Proteomic databases

EPDiQ9BUL8
MaxQBiQ9BUL8
PaxDbiQ9BUL8
PeptideAtlasiQ9BUL8
PRIDEiQ9BUL8
TopDownProteomicsiQ9BUL8

2D gel databases

OGPiQ9BUL8

PTM databases

iPTMnetiQ9BUL8
PhosphoSitePlusiQ9BUL8

Expressioni

Tissue specificityi

Ubiquitous.1 Publication

Gene expression databases

BgeeiENSG00000114209
CleanExiHS_PDCD10
ExpressionAtlasiQ9BUL8 baseline and differential
GenevisibleiQ9BUL8 HS

Organism-specific databases

HPAiHPA027095

Interactioni

Subunit structurei

Homodimer (PubMed:20489202). Interacts (via C-terminus) with CCM2 (PubMed:17360971, PubMed:20489202). Interacts (via C-terminus) with PXN (PubMed:20489202). Interacts (via N-terminus) with STK25 (PubMed:17360971, PubMed:20332113). Interacts (via N-terminus) with STK26 (PubMed:17360971, PubMed:20332113, PubMed:27807006). Interacts (via N-terminus) with STK24 (PubMed:20332113, PubMed:27807006). Interacts with GOLGA2 (PubMed:20332113). Identified in a complex with KRIT1 and CCM2. Interacts with KDR/VEGFR2. Interaction with KDR/VEGFR2 is enhanced by stimulation with VEGFA (By similarity). Interacts with RIPOR1 (via C-terminus); this interaction is required for the association of RIPOR1 with either STK24 and STK26 kinases and occurs in a Rho-independent manner (PubMed:27807006).By similarity4 Publications

Binary interactionsi

Show more details

GO - Molecular functioni

  • protein homodimerization activity Source: UniProtKB
  • protein kinase binding Source: UniProtKB
  • protein N-terminus binding Source: UniProtKB

Protein-protein interaction databases

BioGridi116400, 60 interactors
DIPiDIP-40607N
IntActiQ9BUL8, 36 interactors
MINTiQ9BUL8
STRINGi9606.ENSP00000376506

Structurei

Secondary structure

1212
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi5 – 9Combined sources5
Helixi11 – 14Combined sources4
Helixi17 – 19Combined sources3
Helixi20 – 24Combined sources5
Helixi26 – 34Combined sources9
Helixi38 – 54Combined sources17
Helixi58 – 69Combined sources12
Helixi76 – 82Combined sources7
Turni83 – 85Combined sources3
Helixi88 – 91Combined sources4
Helixi98 – 115Combined sources18
Helixi117 – 120Combined sources4
Beta strandi121 – 123Combined sources3
Helixi124 – 151Combined sources28
Turni152 – 156Combined sources5
Helixi157 – 184Combined sources28
Helixi187 – 208Combined sources22

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3AJMX-ray2.30A/B8-212[»]
3L8IX-ray2.50A/B/C/D1-212[»]
3L8JX-ray3.05A14-212[»]
3RQEX-ray2.80A/B/C/D1-212[»]
3RQFX-ray2.70A/B/C/D1-212[»]
3RQGX-ray2.50A/B/C/D1-212[»]
3W8HX-ray2.43A8-212[»]
3W8IX-ray2.40A8-212[»]
4GEHX-ray1.95A/C9-212[»]
4TVQX-ray2.80A/B/C/D1-212[»]
ProteinModelPortaliQ9BUL8
SMRiQ9BUL8
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9BUL8

Family & Domainsi

Sequence similaritiesi

Belongs to the PDCD10 family.Curated

Phylogenomic databases

eggNOGiKOG4025 Eukaryota
ENOG410XTA6 LUCA
GeneTreeiENSGT00390000017913
HOGENOMiHOG000007888
HOVERGENiHBG052811
InParanoidiQ9BUL8
KOiK18269
OMAiTMGDETP
OrthoDBiEOG091G0JQQ
PhylomeDBiQ9BUL8
TreeFamiTF105802

Family and domain databases

InterProiView protein in InterPro
IPR009652 PDCD10
PANTHERiPTHR13250 PTHR13250, 1 hit

Sequencei

Sequence statusi: Complete.

Q9BUL8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRMTMEEMKN EAETTSMVSM PLYAVMYPVF NELERVNLSA AQTLRAAFIK
60 70 80 90 100
AEKENPGLTQ DIIMKILEKK SVEVNFTESL LRMAADDVEE YMIERPEPEF
110 120 130 140 150
QDLNEKARAL KQILSKIPDE INDRVRFLQT IKDIASAIKE LLDTVNNVFK
160 170 180 190 200
KYQYQNRRAL EHQKKEFVKY SKSFSDTLKT YFKDGKAINV FVSANRLIHQ
210
TNLILQTFKT VA
Length:212
Mass (Da):24,702
Last modified:June 1, 2001 - v1
Checksum:i5AA613F71FAAEF56
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_023578102D → A1 PublicationCorresponds to variant dbSNP:rs1129087Ensembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF022385 mRNA Translation: AAB72225.1
CR457107 mRNA Translation: CAG33388.1
AK291130 mRNA Translation: BAF83819.1
AC079822 Genomic DNA No translation available.
CH471052 Genomic DNA Translation: EAW78574.1
CH471052 Genomic DNA Translation: EAW78575.1
CH471052 Genomic DNA Translation: EAW78576.1
CH471052 Genomic DNA Translation: EAW78577.1
CH471052 Genomic DNA Translation: EAW78578.1
CH471052 Genomic DNA Translation: EAW78580.1
CH471052 Genomic DNA Translation: EAW78581.1
BC002506 mRNA Translation: AAH02506.1
BC016353 mRNA Translation: AAH16353.1
CCDSiCCDS3202.1
RefSeqiNP_009148.2, NM_007217.3
NP_665858.1, NM_145859.1
NP_665859.1, NM_145860.1
XP_005247143.1, XM_005247086.4
XP_005247144.1, XM_005247087.4
XP_005247145.1, XM_005247088.3
XP_006713548.1, XM_006713485.3
XP_011510670.1, XM_011512368.2
XP_011510671.1, XM_011512369.2
XP_016861133.1, XM_017005644.1
UniGeneiHs.478150

Genome annotation databases

EnsembliENST00000392750; ENSP00000376506; ENSG00000114209
ENST00000461494; ENSP00000420021; ENSG00000114209
ENST00000470131; ENSP00000417202; ENSG00000114209
ENST00000473645; ENSP00000418317; ENSG00000114209
ENST00000497056; ENSP00000420553; ENSG00000114209
GeneIDi11235
KEGGihsa:11235
UCSCiuc003fex.5 human

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Entry informationi

Entry nameiPDC10_HUMAN
AccessioniPrimary (citable) accession number: Q9BUL8
Secondary accession number(s): A8K515, D3DNN5, O14811
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 11, 2005
Last sequence update: June 1, 2001
Last modified: May 23, 2018
This is version 141 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 3
    Human chromosome 3: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

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