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Q9BUL8 (PDC10_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 108. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Programmed cell death protein 10
Alternative name(s):
Cerebral cavernous malformations 3 protein
TF-1 cell apoptosis-related protein 15
Gene names
Name:PDCD10
Synonyms:CCM3, TFAR15
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length212 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Promotes cell proliferation. Modulates apoptotic pathways. Increases mitogen-activated protein kinase activity and MST4 activity. Important for cell migration, and for normal structure and assembly of the Golgi complex. 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. Ref.8 Ref.9 Ref.12

Subunit structure

Homodimer. Interacts (via C-terminus) with CCM2 and PXN. Interacts (via N-terminus) with MST4, STK24 and STK25. Interacts with GOLGA2. Identified in a complex with CCM1 and CCM2. Interacts with KDR/VEGFR2. Interaction with KDR/VEGFR2 is enhanced by stimulation with VEGFA By similarity. Ref.9 Ref.10 Ref.12 Ref.15

Subcellular location

Cytoplasm. Golgi apparatus membrane; Peripheral membrane protein; Cytoplasmic side. Cell membrane; Peripheral membrane protein; Cytoplasmic side. Note: Partially co-localizes with endogenous PXN at the leading edges of migrating cells. Ref.9 Ref.12 Ref.15

Tissue specificity

Ubiquitous. Ref.8

Involvement in disease

Cerebral cavernous malformations 3 (CCM3) [MIM:603285]: A 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.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.8

Sequence similarities

Belongs to the PDCD10 family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 212212Programmed cell death protein 10
PRO_0000187562

Amino acid modifications

Modified residue1791N6-acetyllysine Ref.11

Natural variations

Natural variant1021D → A. Ref.1
Corresponds to variant rs1129087 [ dbSNP | Ensembl ].
VAR_023578

Experimental info

Mutagenesis1321K → D: Loss of interaction with CCM2 and PXN; when associated with D-139; D-172 and D-179. Ref.15
Mutagenesis1351A → D: Loss of interaction with CCM2. Ref.15
Mutagenesis1391K → D: Loss of interaction with CCM2 and PXN; when associated with D-132; D-172 and D-179. Ref.15
Mutagenesis1721K → D: Loss of interaction with CCM2 and PXN; when associated with D-132; D-139 and D-179. Ref.15
Mutagenesis1751S → D: Loss of interaction with CCM2. Ref.15
Mutagenesis1791K → D: Loss of interaction with CCM2 and PXN; when associated with D-132; D-139 and D-172. Ref.15

Secondary structure

......................... 212
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9BUL8 [UniParc].

Last modified June 1, 2001. Version 1.
Checksum: 5AA613F71FAAEF56

FASTA21224,702
        10         20         30         40         50         60 
MRMTMEEMKN EAETTSMVSM PLYAVMYPVF NELERVNLSA AQTLRAAFIK AEKENPGLTQ 

        70         80         90        100        110        120 
DIIMKILEKK SVEVNFTESL LRMAADDVEE YMIERPEPEF QDLNEKARAL KQILSKIPDE 

       130        140        150        160        170        180 
INDRVRFLQT IKDIASAIKE LLDTVNNVFK KYQYQNRRAL EHQKKEFVKY SKSFSDTLKT 

       190        200        210 
YFKDGKAINV FVSANRLIHQ TNLILQTFKT VA 

« Hide

References

« Hide 'large scale' references
[1]"cDNA cloning and expression of an apoptosis-related gene, human TFAR-15 gene."
Wang Y.G., Liu H.T., Ma D.L., Zhang Y.M.
Sci. China, Ser. C, Life Sci. 42:323-329(1999)
Cited for: NUCLEOTIDE SEQUENCE [MRNA], VARIANT ALA-102.
[2]"Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.
Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[3]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[4]"The DNA sequence, annotation and analysis of human chromosome 3."
Muzny D.M., Scherer S.E., Kaul R., Wang J., Yu J., Sudbrak R., Buhay C.J., Chen R., Cree A., Ding Y., Dugan-Rocha S., Gill R., Gunaratne P., Harris R.A., Hawes A.C., Hernandez J., Hodgson A.V., Hume J. expand/collapse author list , Jackson A., Khan Z.M., Kovar-Smith C., Lewis L.R., Lozado R.J., Metzker M.L., Milosavljevic A., Miner G.R., Morgan M.B., Nazareth L.V., Scott G., Sodergren E., Song X.-Z., Steffen D., Wei S., Wheeler D.A., Wright M.W., Worley K.C., Yuan Y., Zhang Z., Adams C.Q., Ansari-Lari M.A., Ayele M., Brown M.J., Chen G., Chen Z., Clendenning J., Clerc-Blankenburg K.P., Chen R., Chen Z., Davis C., Delgado O., Dinh H.H., Dong W., Draper H., Ernst S., Fu G., Gonzalez-Garay M.L., Garcia D.K., Gillett W., Gu J., Hao B., Haugen E., Havlak P., He X., Hennig S., Hu S., Huang W., Jackson L.R., Jacob L.S., Kelly S.H., Kube M., Levy R., Li Z., Liu B., Liu J., Liu W., Lu J., Maheshwari M., Nguyen B.-V., Okwuonu G.O., Palmeiri A., Pasternak S., Perez L.M., Phelps K.A., Plopper F.J., Qiang B., Raymond C., Rodriguez R., Saenphimmachak C., Santibanez J., Shen H., Shen Y., Subramanian S., Tabor P.E., Verduzco D., Waldron L., Wang J., Wang J., Wang Q., Williams G.A., Wong G.K.-S., Yao Z., Zhang J., Zhang X., Zhao G., Zhou J., Zhou Y., Nelson D., Lehrach H., Reinhardt R., Naylor S.L., Yang H., Olson M., Weinstock G., Gibbs R.A.
Nature 440:1194-1198(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Skin and Urinary bladder.
[7]Bienvenut W.V., Claeys D.
Submitted (NOV-2005) to UniProtKB
Cited for: PROTEIN SEQUENCE OF 36-45 AND 117-124, IDENTIFICATION BY MASS SPECTROMETRY.
Tissue: Platelet.
[8]"Mutations within the programmed cell death 10 gene cause cerebral cavernous malformations."
Bergametti F., Denier C., Labauge P., Arnoult M., Boetto S., Clanet M., Coubes P., Echenne B., Ibrahim R., Irthum B., Jacquet G., Lonjon M., Moreau J.J., Neau J.P., Parker F., Tremoulet M., Tournier-Lasserve E.
Am. J. Hum. Genet. 76:42-51(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, TISSUE SPECIFICITY, INVOLVEMENT IN CCM3.
[9]"PDCD10 interacts with Ste20-related kinase MST4 to promote cell growth and transformation via modulation of the ERK pathway."
Ma X., Zhao H., Shan J., Long F., Chen Y., Chen Y., Zhang Y., Han X., Ma D.
Mol. Biol. Cell 18:1965-1978(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH MST4, FUNCTION, SUBCELLULAR LOCATION.
[10]"Functional analyses of human and zebrafish 18-amino acid in-frame deletion pave the way for domain mapping of the cerebral cavernous malformation 3 protein."
Voss K., Stahl S., Hogan B.M., Reinders J., Schleider E., Schulte-Merker S., Felbor U.
Hum. Mutat. 30:1003-1011(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH STK25; CCM2 AND MST4, IDENTIFICATION IN A COMPLEX WITH CCM1 AND CCM2.
[11]"Lysine acetylation targets protein complexes and co-regulates major cellular functions."
Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-179, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[12]"CCM3/PDCD10 stabilizes GCKIII proteins to promote Golgi assembly and cell orientation."
Fidalgo M., Fraile M., Pires A., Force T., Pombo C., Zalvide J.
J. Cell Sci. 123:1274-1284(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH GOLGA2; MST4; STK24 AND STK25, SUBCELLULAR LOCATION.
[13]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[14]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[15]"Crystal structure of CCM3, a cerebral cavernous malformation protein critical for vascular integrity."
Li X., Zhang R., Zhang H., He Y., Ji W., Min W., Boggon T.J.
J. Biol. Chem. 285:24099-24107(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS), SUBUNIT, INTERACTION WITH CCM2 AND PXN, SUBCELLULAR LOCATION, MUTAGENESIS OF LYS-132; ALA-135; LYS-139; LYS-172; SER-175 AND LYS-179.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS3202.1.
RefSeqNP_009148.2. NM_007217.3.
NP_665858.1. NM_145859.1.
NP_665859.1. NM_145860.1.
XP_005247143.1. XM_005247086.2.
XP_005247144.1. XM_005247087.2.
XP_005247145.1. XM_005247088.2.
XP_006713548.1. XM_006713485.1.
UniGeneHs.478150.

3D structure databases

PDBe
RCSB-PDB
PDBj
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[»]
ProteinModelPortalQ9BUL8.
SMRQ9BUL8. Positions 11-211.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid116400. 46 interactions.
DIPDIP-40607N.
IntActQ9BUL8. 25 interactions.
MINTMINT-5003501.
STRING9606.ENSP00000338141.

PTM databases

PhosphoSiteQ9BUL8.

Polymorphism databases

DMDM74733232.

2D gel databases

OGPQ9BUL8.

Proteomic databases

MaxQBQ9BUL8.
PaxDbQ9BUL8.
PRIDEQ9BUL8.

Protocols and materials databases

DNASU11235.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000392750; ENSP00000376506; ENSG00000114209.
ENST00000461494; ENSP00000420021; ENSG00000114209.
ENST00000470131; ENSP00000417202; ENSG00000114209.
ENST00000473645; ENSP00000418317; ENSG00000114209.
ENST00000497056; ENSP00000420553; ENSG00000114209.
GeneID11235.
KEGGhsa:11235.
UCSCuc003fex.3. human.

Organism-specific databases

CTD11235.
GeneCardsGC03M167381.
GeneReviewsPDCD10.
HGNCHGNC:8761. PDCD10.
HPAHPA027095.
MIM603285. phenotype.
609118. gene.
neXtProtNX_Q9BUL8.
Orphanet221061. Hereditary cerebral cavernous malformation.
PharmGKBPA33111.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG275788.
HOGENOMHOG000007888.
HOVERGENHBG052811.
InParanoidQ9BUL8.
KOK18269.
OMARIRCHNA.
OrthoDBEOG7ZPNM3.
PhylomeDBQ9BUL8.
TreeFamTF105802.

Gene expression databases

ArrayExpressQ9BUL8.
BgeeQ9BUL8.
CleanExHS_PDCD10.
GenevestigatorQ9BUL8.

Family and domain databases

InterProIPR009652. DUF1241.
[Graphical view]
PANTHERPTHR13250. PTHR13250. 1 hit.
PfamPF06840. DUF1241. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSPDCD10. human.
EvolutionaryTraceQ9BUL8.
GeneWikiPDCD10.
GenomeRNAi11235.
NextBio42758.
PROQ9BUL8.
SOURCESearch...

Entry information

Entry namePDC10_HUMAN
AccessionPrimary (citable) accession number: Q9BUL8
Secondary accession number(s): A8K515, D3DNN5, O14811
Entry history
Integrated into UniProtKB/Swiss-Prot: October 11, 2005
Last sequence update: June 1, 2001
Last modified: July 9, 2014
This is version 108 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 3

Human chromosome 3: entries, gene names and cross-references to MIM