Q96DZ5 (CLIP3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	CLIP3
Synonyms:	CLIPR59

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	547 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Functions as a cytoplasmic linker protein. Involved in TGN-endosome dynamics.
Subunit structure	Homodimer.
Subcellular location	Cytoplasm. Golgi apparatus › Golgi stack. Note: Localized to Golgi stacks as well as on tubulovesicular elements juxtaposed to Golgi cisternae.
Domain	Microtubule association is inhibited by the ANK repeats and the Golgi localization region (GoLD).
Miscellaneous	The N-terminal half is dispensable for proper Golgi targeting, whereas the GoLD region is required.
Sequence similarities	Contains 3 ANK repeats. Contains 2 CAP-Gly domains.

Ontologies

Keywords
Cellular component	Cytoplasm Golgi apparatus
Coding sequence diversity	Polymorphism
Domain	ANK repeat Repeat
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	chaperone-mediated protein transport Inferred from mutant phenotype PubMed 20052288. Source: UniProtKB fat cell differentiation Inferred from sequence or structural similarity. Source: UniProtKB membrane biogenesis Inferred from mutant phenotype Ref.1. Source: UniProtKB negative regulation of microtubule polymerization Inferred from mutant phenotype PubMed 15262990. Source: UniProtKB peptidyl-L-cysteine S-palmitoylation Inferred from mutant phenotype PubMed 15262990. Source: UniProtKB positive regulation of apoptotic process Inferred from mutant phenotype PubMed 20052288. Source: UniProtKB positive regulation of endocytosis Inferred from mutant phenotype Ref.1. Source: UniProtKB positive regulation of establishment of protein localization to plasma membrane Inferred from sequence or structural similarity. Source: UniProtKB positive regulation of glucose transport Inferred from sequence or structural similarity. Source: UniProtKB positive regulation of protein phosphorylation Inferred from sequence or structural similarity. Source: UniProtKB
Cellular_component	Golgi stack Inferred from electronic annotation. Source: UniProtKB-SubCell early endosome membrane Inferred from direct assay Ref.1. Source: UniProtKB membrane raft Inferred from direct assay PubMed 15262990. Source: UniProtKB plasma membrane Inferred from direct assay PubMed 19139280. Source: UniProtKB recycling endosome membrane Inferred from direct assay Ref.1. Source: UniProtKB trans-Golgi network membrane Inferred from direct assay Ref.1. Source: UniProtKB
Molecular_function	ganglioside binding Inferred from direct assay PubMed 20052288. Source: UniProtKB microtubule binding Inferred from direct assay PubMed 15262990. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 547

547

CAP-Gly domain-containing linker protein 3

PRO_0000076212

Regions

Repeat

117 – 158

42

ANK 1

Repeat

160 – 191

32

ANK 2

Repeat

197 – 229

33

ANK 3

Domain

314 – 356

43

CAP-Gly 1

Domain

436 – 478

43

CAP-Gly 2

Region

488 – 547

60

GoLD

Compositional bias

16 – 25

10

Poly-Glu

Natural variations

Natural variant

175

1

D → V. Ref.3
Corresponds to variant rs17851002 [ dbSNP | Ensembl ].

VAR_027962

Secondary structure

1

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547

Helix Strand Turn

Details...

Helix

288 – 292

5

Beta strand

299 – 302

4

Turn

303 – 305

3

Beta strand

306 – 314

9

Beta strand

317 – 319

3

Beta strand

323 – 331

9

Beta strand

337 – 339

3

Beta strand

348 – 350

3

Beta strand

352 – 355

4

Helix

357 – 359

3

Beta strand

360 – 362

3

Sequences

	Sequence		Length	Mass (Da)
	Q96DZ5 [UniParc]. Last modified October 17, 2006. Version 3. Checksum: A718D9673EC1CF4B	FASTA	547	59,560
	10 20 30 40 50 60 MTKTDPAPMA PPPRGEEEEE EEEDEPVPEA PSPTQERRQK PVVHPSAPAP LPKDYAFTFF 70 80 90 100 110 120 DPNDPACQEI LFDPQTTIPE LFAIVRQWVP QVQHKIDVIG NEILRRGCHV NDRDGLTDMT 130 140 150 160 170 180 LLHYACKAGA HGVGDPAAAV RLSQQLLALG ADVTLRSRWT NMNALHYAAY FDVPDLVRVL 190 200 210 220 230 240 LKGARPRVVN STCSDFNHGS ALHIAASSLC LGAAKCLLEH GANPALRNRK GQVPAEVVPD 250 260 270 280 290 300 PMDMSLDKAE AALVAKELRT LLEEAVPLSC ALPKVTLPNY DNVPGNLMLS ALGLRLGDRV 310 320 330 340 350 360 LLDGQKTGTL RFCGTTEFAS GQWVGVELDE PEGKNDGSVG GVRYFICPPK QGLFASVSKI 370 380 390 400 410 420 SKAVDAPPSS VTSTPRTPRM DFSRVTGKGR REHKGKKKTP SSPSLGSLQQ RDGAKAEVGD 430 440 450 460 470 480 QVLVAGQKQG IVRFYGKTDF APGYWYGIEL DQPTGKHDGS VFGVRYFTCP PRHGVFAPAS 490 500 510 520 530 540 RIQRIGGSTD SPGDSVGAKK VHQVTMTQPK RTFTTVRTPK DIASENSISR LLFCCWFPWM LRAEMQS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"CLIPR-59, a new trans-Golgi/TGN cytoplasmic linker protein belonging to the CLIP-170 family." Perez F., Pernet-Gallay K., Nizak C., Goodson H.V., Kreis T.E., Goud B. J. Cell Biol. 156:631-642(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]	"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. , 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]. Tissue: Brain and Cerebellum.
[3]	"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], VARIANT VAL-175. Tissue: Brain and Skin.
[4]	"The full-ORF clone resource of the German cDNA consortium." Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I. BMC Genomics 8:399-399(2007) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 387-547. Tissue: Uterus.
[5]	"Human CLIP-170-related protein CLIPR59." RIKEN structural genomics initiative (RSGI) Submitted (NOV-2005) to the PDB data bank Cited for: STRUCTURE BY NMR OF 285-366.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

IPI

IPI00103362.

PIR

T17253.

RefSeq

NP_001186499.1. NM_001199570.1.
NP_056341.1. NM_015526.2.

UniGene

Hs.466539.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2CP0	NMR	-	A	285-366	[»]

ProteinModelPortal

Q96DZ5.

ModBase

Search...

Protein-protein interaction databases

STRING

9606.ENSP00000353732.

PTM databases

PhosphoSite

Q96DZ5.

Polymorphism databases

DMDM

116241302.

Proteomic databases

PaxDb

Q96DZ5.

PRIDE

Q96DZ5.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000360535; ENSP00000353732; ENSG00000105270.
ENST00000593074; ENSP00000466832; ENSG00000105270.

GeneID

25999.

KEGG

hsa:25999.

UCSC

uc002ocz.2. human.

Organism-specific databases

CTD

25999.

GeneCards

GC19M036505.

H-InvDB

HIX0040341.

HGNC

HGNC:24314. CLIP3.

HPA

HPA041429.

MIM

607382. gene.

neXtProt

NX_Q96DZ5.

PharmGKB

PA162382439.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG5244.

HOGENOM

HOG000007206.

HOVERGEN

HBG057079.

InParanoid

Q96DZ5.

KO

K10423.

OMA

DNVGAKK.

OrthoDB

EOG4Z36DJ.

PhylomeDB

Q96DZ5.

Gene expression databases

ArrayExpress

Q96DZ5.

Bgee

Q96DZ5.

CleanEx

HS_CLIP3.

Genevestigator

Q96DZ5.

GermOnline

ENSG00000105270. Homo sapiens.

Family and domain databases

Gene3D

1.25.40.20. 1 hit.
2.30.30.190. 2 hits.

InterPro

IPR002110. Ankyrin_rpt.
IPR020683. Ankyrin_rpt-contain_dom.
IPR000938. CAP-Gly_domain.
[Graphical view]

Pfam

PF12796. Ank_2. 1 hit.
PF01302. CAP_GLY. 2 hits.
[Graphical view]

SMART

SM00248. ANK. 3 hits.
SM01052. CAP_GLY. 2 hits.
[Graphical view]

SUPFAM

SSF48403. ANK. 1 hit.
SSF74924. CAP-Gly_domain. 2 hits.

PROSITE

PS50297. ANK_REP_REGION. 1 hit.
PS50088. ANK_REPEAT. 1 hit.
PS00845. CAP_GLY_1. 2 hits.
PS50245. CAP_GLY_2. 2 hits.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q96DZ5.

GenomeRNAi

25999.

NextBio

47718.

SOURCE

Search...

Entry information

Entry name

CLIP3_HUMAN

Accession

Primary (citable) accession number: Q96DZ5
Secondary accession number(s): A8K0E4 , Q8WWL1, Q96C99, Q9UFT7

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 10, 2006
Last sequence update:	October 17, 2006
Last modified:	May 1, 2013
This is version 104 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.