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Protein

CAP-Gly domain-containing linker protein 3

Gene

CLIP3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Functions as a cytoplasmic linker protein. Involved in TGN-endosome dynamics. May modulate the cellular compartmentalization of AKT kinase family and promote its cell membrane localization, thereby playing a role in glucose transport in adipocytes.1 Publication

GO - Molecular functioni

  • ganglioside binding Source: UniProtKB
  • microtubule binding Source: UniProtKB

GO - Biological processi

  • chaperone-mediated protein transport Source: UniProtKB
  • fat cell differentiation Source: UniProtKB
  • membrane biogenesis Source: UniProtKB
  • negative regulation of microtubule polymerization Source: UniProtKB
  • peptidyl-L-cysteine S-palmitoylation Source: UniProtKB
  • positive regulation of apoptotic process Source: UniProtKB
  • positive regulation of endocytosis Source: UniProtKB
  • positive regulation of establishment of protein localization to plasma membrane Source: UniProtKB
  • positive regulation of glucose transport Source: UniProtKB
  • positive regulation of protein phosphorylation Source: UniProtKB
  • regulation of tumor necrosis factor-mediated signaling pathway Source: Reactome
Complete GO annotation...

Enzyme and pathway databases

ReactomeiR-HSA-5357905. Regulation of TNFR1 signaling.

Names & Taxonomyi

Protein namesi
Recommended name:
CAP-Gly domain-containing linker protein 3
Alternative name(s):
Cytoplasmic linker protein 170-related 59 kDa protein
Short name:
CLIP-170-related 59 kDa protein
Short name:
CLIPR-59
Gene namesi
Name:CLIP3
Synonyms:CLIPR59
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 19

Organism-specific databases

HGNCiHGNC:24314. CLIP3.

Subcellular locationi

  • Cell membrane 1 Publication; Lipid-anchor 1 Publication
  • Cytoplasm 1 Publication
  • Golgi apparatusGolgi stack 1 Publication

  • Note: Localized to Golgi stacks as well as on tubulovesicular elements juxtaposed to Golgi cisternae.

GO - Cellular componenti

  • cytosol Source: Reactome
  • early endosome membrane Source: UniProtKB
  • Golgi stack Source: UniProtKB-SubCell
  • membrane raft Source: UniProtKB
  • plasma membrane Source: UniProtKB
  • recycling endosome membrane Source: UniProtKB
  • trans-Golgi network Source: UniProtKB
  • trans-Golgi network membrane Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Cytoplasm, Golgi apparatus, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi509P → A: Inhibits interaction with ZDHHC13 and ZDHHC17. 1 Publication1
Mutagenesisi534 – 535CC → AA: Strongly reduced plasma membrane association and decrease in the levels of Akt at the plasma membrane. 1 Publication2

Organism-specific databases

OpenTargetsiENSG00000105270.
PharmGKBiPA162382439.

Polymorphism and mutation databases

BioMutaiCLIP3.
DMDMi116241302.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000762121 – 547CAP-Gly domain-containing linker protein 3Add BLAST547

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei374PhosphothreonineBy similarity1
Modified residuei401PhosphoserineBy similarity1
Lipidationi534S-palmitoyl cysteine1 Publication1
Lipidationi535S-palmitoyl cysteine1 Publication1

Post-translational modificationi

Palmitoylation by ZDHHC17 regulates association with the plasma membrane.1 Publication

Keywords - PTMi

Lipoprotein, Palmitate, Phosphoprotein

Proteomic databases

EPDiQ96DZ5.
PaxDbiQ96DZ5.
PeptideAtlasiQ96DZ5.
PRIDEiQ96DZ5.

PTM databases

iPTMnetiQ96DZ5.
PhosphoSitePlusiQ96DZ5.
SwissPalmiQ96DZ5.

Expressioni

Gene expression databases

BgeeiENSG00000105270.
CleanExiHS_CLIP3.
ExpressionAtlasiQ96DZ5. baseline and differential.
GenevisibleiQ96DZ5. HS.

Organism-specific databases

HPAiHPA058298.

Interactioni

Subunit structurei

Homodimer. Interacts with AKT1 and AKT2; when AKT1 and AKT2 are phosphorylated and activated, affinity is higher for AKT2 (PubMed:19139280). Interacts with ZDHHC13 (via ANK repeats) (PubMed:26198635). Interacts with ZDHHC17 (via ANK repeats) (PubMed:26198635).2 Publications

GO - Molecular functioni

  • microtubule binding Source: UniProtKB

Protein-protein interaction databases

BioGridi117475. 9 interactors.
STRINGi9606.ENSP00000353732.

Structurei

Secondary structure

1547
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi288 – 292Combined sources5
Beta strandi299 – 302Combined sources4
Turni303 – 305Combined sources3
Beta strandi306 – 314Combined sources9
Beta strandi317 – 319Combined sources3
Beta strandi323 – 331Combined sources9
Beta strandi337 – 339Combined sources3
Beta strandi348 – 350Combined sources3
Beta strandi352 – 355Combined sources4
Helixi357 – 359Combined sources3
Beta strandi360 – 362Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2CP0NMR-A285-366[»]
ProteinModelPortaliQ96DZ5.
SMRiQ96DZ5.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ96DZ5.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati117 – 158ANK 1Add BLAST42
Repeati160 – 191ANK 2Add BLAST32
Repeati197 – 229ANK 3Add BLAST33
Domaini314 – 356CAP-Gly 1PROSITE-ProRule annotationAdd BLAST43
Domaini436 – 478CAP-Gly 2PROSITE-ProRule annotationAdd BLAST43

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni488 – 547GoLDAdd BLAST60

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi16 – 25Poly-Glu10

Domaini

Microtubule association is inhibited by the ANK repeats and the Golgi localization region (GoLD).

Sequence similaritiesi

Contains 3 ANK repeats.PROSITE-ProRule annotation
Contains 2 CAP-Gly domains.PROSITE-ProRule annotation

Keywords - Domaini

ANK repeat, Repeat

Phylogenomic databases

eggNOGiKOG4568. Eukaryota.
COG5244. LUCA.
GeneTreeiENSGT00760000119173.
HOGENOMiHOG000007206.
HOVERGENiHBG057079.
InParanoidiQ96DZ5.
KOiK10423.
OMAiDNVGAKK.
OrthoDBiEOG091G04NK.
PhylomeDBiQ96DZ5.
TreeFamiTF326096.

Family and domain databases

Gene3Di1.25.40.20. 1 hit.
2.30.30.190. 2 hits.
InterProiIPR002110. Ankyrin_rpt.
IPR020683. Ankyrin_rpt-contain_dom.
IPR000938. CAP-Gly_domain.
IPR030504. CLIP3.
[Graphical view]
PANTHERiPTHR18916:SF11. PTHR18916:SF11. 1 hit.
PfamiPF12796. Ank_2. 1 hit.
PF01302. CAP_GLY. 2 hits.
[Graphical view]
SMARTiSM00248. ANK. 3 hits.
SM01052. CAP_GLY. 2 hits.
[Graphical view]
SUPFAMiSSF48403. SSF48403. 1 hit.
SSF74924. SSF74924. 2 hits.
PROSITEiPS50297. ANK_REP_REGION. 1 hit.
PS50088. ANK_REPEAT. 1 hit.
PS00845. CAP_GLY_1. 2 hits.
PS50245. CAP_GLY_2. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q96DZ5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTKTDPAPMA PPPRGEEEEE EEEDEPVPEA PSPTQERRQK PVVHPSAPAP
60 70 80 90 100
LPKDYAFTFF DPNDPACQEI LFDPQTTIPE LFAIVRQWVP QVQHKIDVIG
110 120 130 140 150
NEILRRGCHV NDRDGLTDMT LLHYACKAGA HGVGDPAAAV RLSQQLLALG
160 170 180 190 200
ADVTLRSRWT NMNALHYAAY FDVPDLVRVL LKGARPRVVN STCSDFNHGS
210 220 230 240 250
ALHIAASSLC LGAAKCLLEH GANPALRNRK GQVPAEVVPD PMDMSLDKAE
260 270 280 290 300
AALVAKELRT LLEEAVPLSC ALPKVTLPNY DNVPGNLMLS ALGLRLGDRV
310 320 330 340 350
LLDGQKTGTL RFCGTTEFAS GQWVGVELDE PEGKNDGSVG GVRYFICPPK
360 370 380 390 400
QGLFASVSKI SKAVDAPPSS VTSTPRTPRM DFSRVTGKGR REHKGKKKTP
410 420 430 440 450
SSPSLGSLQQ RDGAKAEVGD QVLVAGQKQG IVRFYGKTDF APGYWYGIEL
460 470 480 490 500
DQPTGKHDGS VFGVRYFTCP PRHGVFAPAS RIQRIGGSTD SPGDSVGAKK
510 520 530 540
VHQVTMTQPK RTFTTVRTPK DIASENSISR LLFCCWFPWM LRAEMQS
Length:547
Mass (Da):59,560
Last modified:October 17, 2006 - v3
Checksum:iA718D9673EC1CF4B
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_027962175D → V.1 PublicationCorresponds to variant rs17851002dbSNPEnsembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ427922 mRNA. Translation: CAD20873.1.
AK094738 mRNA. Translation: BAG52921.1.
AK289509 mRNA. Translation: BAF82198.1.
BC013116 mRNA. Translation: AAH13116.2.
BC014486 mRNA. Translation: AAH14486.2.
AL117468 mRNA. Translation: CAB55943.1.
CCDSiCCDS12486.1.
PIRiT17253.
RefSeqiNP_001186499.1. NM_001199570.1.
NP_056341.1. NM_015526.2.
UniGeneiHs.466539.

Genome annotation databases

EnsembliENST00000360535; ENSP00000353732; ENSG00000105270.
ENST00000593074; ENSP00000466832; ENSG00000105270.
GeneIDi25999.
KEGGihsa:25999.
UCSCiuc002ocz.3. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ427922 mRNA. Translation: CAD20873.1.
AK094738 mRNA. Translation: BAG52921.1.
AK289509 mRNA. Translation: BAF82198.1.
BC013116 mRNA. Translation: AAH13116.2.
BC014486 mRNA. Translation: AAH14486.2.
AL117468 mRNA. Translation: CAB55943.1.
CCDSiCCDS12486.1.
PIRiT17253.
RefSeqiNP_001186499.1. NM_001199570.1.
NP_056341.1. NM_015526.2.
UniGeneiHs.466539.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2CP0NMR-A285-366[»]
ProteinModelPortaliQ96DZ5.
SMRiQ96DZ5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi117475. 9 interactors.
STRINGi9606.ENSP00000353732.

PTM databases

iPTMnetiQ96DZ5.
PhosphoSitePlusiQ96DZ5.
SwissPalmiQ96DZ5.

Polymorphism and mutation databases

BioMutaiCLIP3.
DMDMi116241302.

Proteomic databases

EPDiQ96DZ5.
PaxDbiQ96DZ5.
PeptideAtlasiQ96DZ5.
PRIDEiQ96DZ5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000360535; ENSP00000353732; ENSG00000105270.
ENST00000593074; ENSP00000466832; ENSG00000105270.
GeneIDi25999.
KEGGihsa:25999.
UCSCiuc002ocz.3. human.

Organism-specific databases

CTDi25999.
GeneCardsiCLIP3.
H-InvDBHIX0040341.
HGNCiHGNC:24314. CLIP3.
HPAiHPA058298.
MIMi607382. gene.
neXtProtiNX_Q96DZ5.
OpenTargetsiENSG00000105270.
PharmGKBiPA162382439.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG4568. Eukaryota.
COG5244. LUCA.
GeneTreeiENSGT00760000119173.
HOGENOMiHOG000007206.
HOVERGENiHBG057079.
InParanoidiQ96DZ5.
KOiK10423.
OMAiDNVGAKK.
OrthoDBiEOG091G04NK.
PhylomeDBiQ96DZ5.
TreeFamiTF326096.

Enzyme and pathway databases

ReactomeiR-HSA-5357905. Regulation of TNFR1 signaling.

Miscellaneous databases

EvolutionaryTraceiQ96DZ5.
GenomeRNAii25999.
PROiQ96DZ5.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000105270.
CleanExiHS_CLIP3.
ExpressionAtlasiQ96DZ5. baseline and differential.
GenevisibleiQ96DZ5. HS.

Family and domain databases

Gene3Di1.25.40.20. 1 hit.
2.30.30.190. 2 hits.
InterProiIPR002110. Ankyrin_rpt.
IPR020683. Ankyrin_rpt-contain_dom.
IPR000938. CAP-Gly_domain.
IPR030504. CLIP3.
[Graphical view]
PANTHERiPTHR18916:SF11. PTHR18916:SF11. 1 hit.
PfamiPF12796. Ank_2. 1 hit.
PF01302. CAP_GLY. 2 hits.
[Graphical view]
SMARTiSM00248. ANK. 3 hits.
SM01052. CAP_GLY. 2 hits.
[Graphical view]
SUPFAMiSSF48403. SSF48403. 1 hit.
SSF74924. SSF74924. 2 hits.
PROSITEiPS50297. ANK_REP_REGION. 1 hit.
PS50088. ANK_REPEAT. 1 hit.
PS00845. CAP_GLY_1. 2 hits.
PS50245. CAP_GLY_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiCLIP3_HUMAN
AccessioniPrimary (citable) accession number: Q96DZ5
Secondary accession number(s): A8K0E4
, Q8WWL1, Q96C99, Q9UFT7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 10, 2006
Last sequence update: October 17, 2006
Last modified: November 2, 2016
This is version 135 of the entry and version 3 of the sequence. [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

Miscellaneous

The N-terminal half is dispensable for proper Golgi targeting, whereas the GoLD region is required.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 19
    Human chromosome 19: 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

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.