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P48059 (LIMS1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 146. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
LIM and senescent cell antigen-like-containing domain protein 1
Alternative name(s):
Particularly interesting new Cys-His protein 1
Short name=PINCH-1
Renal carcinoma antigen NY-REN-48
Gene names
Name:LIMS1
Synonyms:PINCH, PINCH1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length325 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Adapter protein in a cytoplasmic complex linking beta-integrins to the actin cytoskeleton, bridges the complex to cell surface receptor tyrosine kinases and growth factor receptors. Involved in the regulation of cell survival, cell proliferation and cell differentiation.

Subunit structure

Interacts (via LIM zinc-binding 5) with TGFB1I1 By similarity. Interacts with integrin-linked protein kinase 1 (ILK) via the first LIM domain, and in competition with LIMS2. Part of the heterotrimeric IPP complex composed of integrin-linked kinase (ILK), LIMS1 or LIMS2, and PARVA. Interacts with SH3/SH2 adapter NCK2, thereby linking the complex to cell surface receptors. Ref.7 Ref.9

Subcellular location

Cell junctionfocal adhesion. Cell membrane; Peripheral membrane protein; Cytoplasmic side Ref.9 Ref.15.

Tissue specificity

Expressed in most tissues except in the brain.

Sequence similarities

Contains 5 LIM zinc-binding domains.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Hoxa1P090223EBI-306928,EBI-3957603From a different organism.
ILKQ134185EBI-306928,EBI-747644
IlkO552223EBI-306928,EBI-6690138From a different organism.
NCK2O436392EBI-306928,EBI-713635

Alternative products

This entry describes 5 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: P48059-1)

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.
Isoform 2 (identifier: P48059-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MLGVAAGMTHSNM
Note: No experimental confirmation available.
Isoform 3 (identifier: P48059-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MAFSGRARPCIIPENEEIPRAALNTVHEANGTEDERAVSKLQRRHSDVKVYKEFCDFYAKFNM
Isoform 4 (identifier: P48059-4)

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MTCNM
Isoform 5 (identifier: P48059-5)

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MTALQLKELSHSGLYRRRRDRPDSLRVNGLPEEELSNM

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.6
Chain2 – 325324LIM and senescent cell antigen-like-containing domain protein 1
PRO_0000075888

Regions

Domain10 – 6253LIM zinc-binding 1
Domain71 – 12151LIM zinc-binding 2
Domain135 – 18450LIM zinc-binding 3
Domain193 – 24351LIM zinc-binding 4
Domain252 – 30352LIM zinc-binding 5

Amino acid modifications

Modified residue21N-acetylalanine Ref.6

Natural variations

Alternative sequence11M → MLGVAAGMTHSNM in isoform 2.
VSP_042672
Alternative sequence11M → MAFSGRARPCIIPENEEIPR AALNTVHEANGTEDERAVSK LQRRHSDVKVYKEFCDFYAK FNM in isoform 3.
VSP_043210
Alternative sequence11M → MTCNM in isoform 4.
VSP_043211
Alternative sequence11M → MTALQLKELSHSGLYRRRRD RPDSLRVNGLPEEELSNM in isoform 5.
VSP_043212

Experimental info

Mutagenesis421F → A: Loss of interaction with ILK and loss of localization to focal adhesion. Ref.14 Ref.15
Mutagenesis561R → A: Alters interaction with ILK. Ref.15
Mutagenesis611H → D: Alters interaction with ILK. Ref.14
Mutagenesis621D → A: Alters interaction with ILK. Ref.14
Mutagenesis661L → D: Alters interaction with ILK. Ref.14
Sequence conflict781I → T in AAH05341. Ref.5
Sequence conflict2621D → G in AAH05341. Ref.5

Secondary structure

................................................................. 325
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified January 23, 2007. Version 4.
Checksum: E665FEB11D849CAE

FASTA32537,251
        10         20         30         40         50         60 
MANALASATC ERCKGGFAPA EKIVNSNGEL YHEQCFVCAQ CFQQFPEGLF YEFEGRKYCE 

        70         80         90        100        110        120 
HDFQMLFAPC CHQCGEFIIG RVIKAMNNSW HPECFRCDLC QEVLADIGFV KNAGRHLCRP 

       130        140        150        160        170        180 
CHNREKARGL GKYICQKCHA IIDEQPLIFK NDPYHPDHFN CANCGKELTA DARELKGELY 

       190        200        210        220        230        240 
CLPCHDKMGV PICGACRRPI EGRVVNAMGK QWHVEHFVCA KCEKPFLGHR HYERKGLAYC 

       250        260        270        280        290        300 
ETHYNQLFGD VCFHCNRVIE GDVVSALNKA WCVNCFACST CNTKLTLKNK FVEFDMKPVC 

       310        320 
KKCYEKFPLE LKKRLKKLAE TLGRK 

« Hide

Isoform 2 [UniParc].

Checksum: 8577792E1A56418B
Show »

FASTA33738,422
Isoform 3 [UniParc].

Checksum: 3AB2EDB2203CEBFF
Show »

FASTA38744,390
Isoform 4 [UniParc].

Checksum: A69518B2E12F39A5
Show »

FASTA32937,701
Isoform 5 [UniParc].

Checksum: B2123BE2DDC4736C
Show »

FASTA36241,571

References

« Hide 'large scale' references
[1]"A new LIM protein containing an autoepitope homologous to 'senescent cell antigen'."
Rearden A.
Biochem. Biophys. Res. Commun. 201:1124-1131(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
Tissue: Fetal liver.
[2]Rearden A.
Submitted (MAR-2001) to the EMBL/GenBank/DDBJ databases
Cited for: SEQUENCE REVISION TO C-TERMINUS.
[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] (ISOFORMS 1; 2; 3 AND 5).
Tissue: Testis, Tongue and Trachea.
[4]"Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H. expand/collapse author list , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"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] (ISOFORM 1).
Tissue: Bone marrow.
[6]"Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides."
Gevaert K., Goethals M., Martens L., Van Damme J., Staes A., Thomas G.R., Vandekerckhove J.
Nat. Biotechnol. 21:566-569(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 2-12, ACETYLATION AT ALA-2.
Tissue: Platelet.
[7]"Nck-2, a novel Src homology2/3-containing adaptor protein that interacts with the LIM-only protein PINCH and components of growth factor receptor kinase-signaling pathways."
Tu Y., Li F., Wu C.
Mol. Biol. Cell 9:3367-3382(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH NCK2.
[8]"Antigens recognized by autologous antibody in patients with renal-cell carcinoma."
Scanlan M.J., Gordan J.D., Williamson B., Stockert E., Bander N.H., Jongeneel C.V., Gure A.O., Jaeger D., Jaeger E., Knuth A., Chen Y.-T., Old L.J.
Int. J. Cancer 83:456-464(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION AS A RENAL CANCER ANTIGEN.
Tissue: Renal cell carcinoma.
[9]"The LIM-only protein PINCH directly interacts with integrin-linked kinase and is recruited to integrin-rich sites in spreading cells."
Tu Y., Li F., Goicoechea S., Wu C.
Mol. Cell. Biol. 19:2425-2434(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH ILK AND NCK2, SUBCELLULAR LOCATION.
[10]"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].
[11]"Solution structure of the focal adhesion adaptor PINCH LIM1 domain and characterization of its interaction with the integrin-linked kinase ankyrin repeat domain."
Velyvis A., Yang Y., Wu C., Qin J.
J. Biol. Chem. 276:4932-4939(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 1-70.
[12]"Structural and functional insights into PINCH LIM4 domain-mediated integrin signaling."
Velyvis A., Vaynberg J., Yang Y., Vinogradova O., Zhang Y., Wu C., Qin J.
Nat. Struct. Biol. 10:558-564(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 188-251.
[13]"Solution structure of the second and third LIM domain of particularly interesting new Cys-His protein (PINCH)."
RIKEN structural genomics initiative (RSGI)
Submitted (JUN-2006) to the PDB data bank
Cited for: STRUCTURE BY NMR OF 71-190.
[14]"The structural basis of integrin-linked kinase-PINCH interactions."
Chiswell B.P., Zhang R., Murphy J.W., Boggon T.J., Calderwood D.A.
Proc. Natl. Acad. Sci. U.S.A. 105:20677-20682(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 6-68 IN COMPLEX WITH ILK, MUTAGENESIS OF PHE-42; HIS-61; ASP-62 AND LEU-66.
[15]"Structural basis of focal adhesion localization of LIM-only adaptor PINCH by integrin-linked kinase."
Yang Y., Wang X., Hawkins C.A., Chen K., Vaynberg J., Mao X., Tu Y., Zuo X., Wang J., Wang Y.-X., Wu C., Tjandra N., Qin J.
J. Biol. Chem. 284:5836-5844(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 1-70 IN COMPLEX WITH ILK, MUTAGENESIS OF PHE-42 AND ARG-56, SUBCELLULAR LOCATION.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U09284 mRNA. Translation: AAA20086.2.
AK296992 mRNA. Translation: BAH12469.1.
AK302411 mRNA. Translation: BAH13699.1.
AK304260 mRNA. Translation: BAH14143.1.
AK314217 mRNA. Translation: BAG36891.1.
AC010095 Genomic DNA. Translation: AAY14983.1.
AC012487 Genomic DNA. No translation available.
BC005341 mRNA. Translation: AAH05341.1.
PIRJC2324.
RefSeqNP_001180411.1. NM_001193482.1.
NP_001180412.1. NM_001193483.2.
NP_001180413.1. NM_001193484.1.
NP_001180414.1. NM_001193485.2.
NP_001180417.1. NM_001193488.1.
NP_004978.2. NM_004987.5.
UniGeneHs.597715.
Hs.613268.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1G47NMR-A1-70[»]
1NYPNMR-A188-251[»]
1U5SNMR-B188-251[»]
2CORNMR-A125-190[»]
2D8XNMR-A71-126[»]
2KBXNMR-B1-70[»]
3F6QX-ray1.60B6-68[»]
4HI8X-ray1.20B6-68[»]
4HI9X-ray1.20B6-68[»]
ProteinModelPortalP48059.
SMRP48059. Positions 6-307.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid110175. 14 interactions.
DIPDIP-40671N.
IntActP48059. 29 interactions.
MINTMINT-5004275.
STRING9606.ENSP00000331775.

PTM databases

PhosphoSiteP48059.

Polymorphism databases

DMDM18266876.

2D gel databases

OGPP48059.

Proteomic databases

PaxDbP48059.
PRIDEP48059.

Protocols and materials databases

DNASU3987.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000332345; ENSP00000331775; ENSG00000169756. [P48059-1]
ENST00000338045; ENSP00000337598; ENSG00000169756. [P48059-1]
ENST00000393310; ENSP00000376987; ENSG00000169756. [P48059-1]
ENST00000409441; ENSP00000387264; ENSG00000169756. [P48059-5]
ENST00000410093; ENSP00000386926; ENSG00000169756. [P48059-4]
ENST00000542845; ENSP00000446121; ENSG00000169756. [P48059-3]
ENST00000544547; ENSP00000437912; ENSG00000169756. [P48059-2]
GeneID3987.
KEGGhsa:3987.
UCSCuc002teg.3. human. [P48059-1]
uc002tei.3. human. [P48059-4]
uc002tej.3. human. [P48059-5]
uc002tek.4. human. [P48059-3]
uc002tel.3. human. [P48059-2]

Organism-specific databases

CTD3987.
GeneCardsGC02P109150.
HGNCHGNC:6616. LIMS1.
MIM602567. gene.
neXtProtNX_P48059.
PharmGKBPA30389.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG263350.
HOGENOMHOG000253950.
HOVERGENHBG000053.
InParanoidP48059.
OMANQNRALC.
PhylomeDBP48059.
TreeFamTF314113.

Enzyme and pathway databases

ReactomeREACT_111155. Cell-Cell communication.

Gene expression databases

ArrayExpressP48059.
BgeeP48059.
CleanExHS_LIMS1.
GenevestigatorP48059.

Family and domain databases

Gene3D2.10.110.10. 5 hits.
InterProIPR017351. PINCH.
IPR001781. Znf_LIM.
[Graphical view]
PANTHERPTHR24210. PTHR24210. 1 hit.
PfamPF00412. LIM. 5 hits.
[Graphical view]
PIRSFPIRSF038003. PINCH. 1 hit.
SMARTSM00132. LIM. 5 hits.
[Graphical view]
PROSITEPS00478. LIM_DOMAIN_1. 4 hits.
PS50023. LIM_DOMAIN_2. 5 hits.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSLIMS1. human.
EvolutionaryTraceP48059.
GeneWikiLIMS1.
GenomeRNAi3987.
NextBio15640.
PROP48059.
SOURCESearch...

Entry information

Entry nameLIMS1_HUMAN
AccessionPrimary (citable) accession number: P48059
Secondary accession number(s): B2RAJ4 expand/collapse secondary AC list , B7Z483, B7Z7R3, B7Z907, Q53TE0, Q9BS44
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: January 23, 2007
Last modified: April 16, 2014
This is version 146 of the entry and version 4 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 chromosome 2

Human chromosome 2: entries, gene names and cross-references to MIM