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Protein

LIM and senescent cell antigen-like-containing domain protein 1

Gene

LIMS1

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

Functioni

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.

GO - Molecular functioni

  • protein kinase binding Source: UniProtKB
  • zinc ion binding Source: UniProtKB

GO - Biological processi

  • cell aging Source: ProtInc
  • cell junction assembly Source: Reactome
  • cellular response to transforming growth factor beta stimulus Source: UniProtKB
  • establishment of protein localization Source: UniProtKB
  • negative regulation of transcription, DNA-templated Source: UniProtKB
  • positive regulation of cell-substrate adhesion Source: UniProtKB
  • positive regulation of focal adhesion assembly Source: UniProtKB
  • positive regulation of gene expression Source: UniProtKB
  • positive regulation of GTPase activity Source: UniProtKB
  • positive regulation of substrate adhesion-dependent cell spreading Source: UniProtKB
Complete GO annotation...

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciZFISH:ENSG00000169756-MONOMER.
ReactomeiR-HSA-446353. Cell-extracellular matrix interactions.
R-HSA-446388. Regulation of cytoskeletal remodeling and cell spreading by IPP complex components.

Names & Taxonomyi

Protein namesi
Recommended 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 namesi
Name:LIMS1
Synonyms:PINCH, PINCH1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

HGNCiHGNC:6616. LIMS1.

Subcellular locationi

GO - Cellular componenti

  • cell-cell junction Source: UniProtKB
  • cytosol Source: Reactome
  • focal adhesion Source: UniProtKB
  • perinuclear region of cytoplasm Source: UniProtKB
  • plasma membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cell junction, Cell membrane, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi42F → A: Loss of interaction with ILK and loss of localization to focal adhesion. 2 Publications1
Mutagenesisi56R → A: Alters interaction with ILK. 1 Publication1
Mutagenesisi61H → D: Alters interaction with ILK. 1 Publication1
Mutagenesisi62D → A: Alters interaction with ILK. 1 Publication1
Mutagenesisi66L → D: Alters interaction with ILK. 1 Publication1

Organism-specific databases

DisGeNETi3987.
OpenTargetsiENSG00000169756.
PharmGKBiPA30389.

Polymorphism and mutation databases

BioMutaiLIMS1.
DMDMi18266876.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00000758882 – 325LIM and senescent cell antigen-like-containing domain protein 1Add BLAST324

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanine1 Publication1

Keywords - PTMi

Acetylation

Proteomic databases

EPDiP48059.
MaxQBiP48059.
PaxDbiP48059.
PeptideAtlasiP48059.
PRIDEiP48059.

2D gel databases

OGPiP48059.

PTM databases

iPTMnetiP48059.
PhosphoSitePlusiP48059.

Expressioni

Tissue specificityi

Expressed in most tissues except in the brain.

Gene expression databases

BgeeiENSG00000169756.
CleanExiHS_LIMS1.
ExpressionAtlasiP48059. baseline and differential.
GenevisibleiP48059. HS.

Organism-specific databases

HPAiHPA058455.

Interactioni

Subunit structurei

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.By similarity4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
Hoxa1P090223EBI-306928,EBI-3957603From a different organism.
ILKQ134187EBI-306928,EBI-747644
IlkO552223EBI-306928,EBI-6690138From a different organism.
NCK2O436392EBI-306928,EBI-713635
RSU1Q154044EBI-306928,EBI-1057132

GO - Molecular functioni

  • protein kinase binding Source: UniProtKB

Protein-protein interaction databases

BioGridi110175. 37 interactors.
DIPiDIP-40671N.
IntActiP48059. 37 interactors.
MINTiMINT-5004275.
STRINGi9606.ENSP00000446121.

Structurei

Secondary structure

1325
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni11 – 13Combined sources3
Beta strandi22 – 26Combined sources5
Beta strandi29 – 32Combined sources4
Turni33 – 35Combined sources3
Turni39 – 41Combined sources3
Helixi46 – 48Combined sources3
Beta strandi51 – 53Combined sources3
Beta strandi56 – 58Combined sources3
Helixi60 – 66Combined sources7
Beta strandi72 – 74Combined sources3
Beta strandi83 – 85Combined sources3
Beta strandi88 – 90Combined sources3
Turni92 – 94Combined sources3
Beta strandi98 – 100Combined sources3
Beta strandi105 – 107Combined sources3
Beta strandi110 – 112Combined sources3
Beta strandi115 – 117Combined sources3
Helixi119 – 126Combined sources8
Turni136 – 138Combined sources3
Beta strandi150 – 152Combined sources3
Turni156 – 158Combined sources3
Beta strandi162 – 164Combined sources3
Beta strandi173 – 175Combined sources3
Beta strandi178 – 180Combined sources3
Helixi182 – 186Combined sources5
Turni194 – 197Combined sources4
Beta strandi210 – 213Combined sources4
Turni214 – 216Combined sources3
Turni220 – 222Combined sources3
Beta strandi227 – 229Combined sources3
Beta strandi232 – 234Combined sources3
Beta strandi237 – 239Combined sources3
Helixi241 – 247Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1G47NMR-A1-70[»]
1NYPNMR-A188-251[»]
1U5SNMR-B188-251[»]
2CORNMR-A125-190[»]
2D8XNMR-A71-127[»]
2KBXNMR-B1-70[»]
3F6QX-ray1.60B6-68[»]
4HI8X-ray1.20B6-68[»]
4HI9X-ray1.20B6-68[»]
ProteinModelPortaliP48059.
SMRiP48059.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP48059.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini10 – 62LIM zinc-binding 1PROSITE-ProRule annotationAdd BLAST53
Domaini71 – 121LIM zinc-binding 2PROSITE-ProRule annotationAdd BLAST51
Domaini135 – 184LIM zinc-binding 3PROSITE-ProRule annotationAdd BLAST50
Domaini193 – 243LIM zinc-binding 4PROSITE-ProRule annotationAdd BLAST51
Domaini252 – 303LIM zinc-binding 5PROSITE-ProRule annotationAdd BLAST52

Sequence similaritiesi

Contains 5 LIM zinc-binding domains.PROSITE-ProRule annotation

Keywords - Domaini

LIM domain, Repeat

Phylogenomic databases

eggNOGiKOG2272. Eukaryota.
ENOG410XP46. LUCA.
GeneTreeiENSGT00760000118910.
HOGENOMiHOG000253950.
HOVERGENiHBG000053.
InParanoidiP48059.
OMAiHFNCTAC.
OrthoDBiEOG091G08K3.
PhylomeDBiP48059.
TreeFamiTF314113.

Family and domain databases

Gene3Di2.10.110.10. 5 hits.
InterProiIPR017351. PINCH.
IPR001781. Znf_LIM.
[Graphical view]
PANTHERiPTHR24210. PTHR24210. 1 hit.
PfamiPF00412. LIM. 5 hits.
[Graphical view]
PIRSFiPIRSF038003. PINCH. 1 hit.
SMARTiSM00132. LIM. 5 hits.
[Graphical view]
PROSITEiPS00478. LIM_DOMAIN_1. 4 hits.
PS50023. LIM_DOMAIN_2. 5 hits.
[Graphical view]

Sequences (5)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P48059-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MANALASATC ERCKGGFAPA EKIVNSNGEL YHEQCFVCAQ CFQQFPEGLF
60 70 80 90 100
YEFEGRKYCE HDFQMLFAPC CHQCGEFIIG RVIKAMNNSW HPECFRCDLC
110 120 130 140 150
QEVLADIGFV KNAGRHLCRP CHNREKARGL GKYICQKCHA IIDEQPLIFK
160 170 180 190 200
NDPYHPDHFN CANCGKELTA DARELKGELY CLPCHDKMGV PICGACRRPI
210 220 230 240 250
EGRVVNAMGK QWHVEHFVCA KCEKPFLGHR HYERKGLAYC ETHYNQLFGD
260 270 280 290 300
VCFHCNRVIE GDVVSALNKA WCVNCFACST CNTKLTLKNK FVEFDMKPVC
310 320
KKCYEKFPLE LKKRLKKLAE TLGRK
Length:325
Mass (Da):37,251
Last modified:January 23, 2007 - v4
Checksum:iE665FEB11D849CAE
GO
Isoform 2 (identifier: P48059-2) [UniParc]FASTAAdd to basket

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

Note: No experimental confirmation available.
Show »
Length:337
Mass (Da):38,422
Checksum:i8577792E1A56418B
GO
Isoform 3 (identifier: P48059-3) [UniParc]FASTAAdd to basket

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

Show »
Length:387
Mass (Da):44,390
Checksum:i3AB2EDB2203CEBFF
GO
Isoform 4 (identifier: P48059-4) [UniParc]FASTAAdd to basket

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

Show »
Length:329
Mass (Da):37,701
Checksum:iA69518B2E12F39A5
GO
Isoform 5 (identifier: P48059-5) [UniParc]FASTAAdd to basket

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

Show »
Length:362
Mass (Da):41,571
Checksum:iB2123BE2DDC4736C
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti78I → T in AAH05341 (PubMed:15489334).Curated1
Sequence conflicti262D → G in AAH05341 (PubMed:15489334).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0426721M → MLGVAAGMTHSNM in isoform 2. 1 Publication1
Alternative sequenceiVSP_0432101M → MAFSGRARPCIIPENEEIPR AALNTVHEANGTEDERAVSK LQRRHSDVKVYKEFCDFYAK FNM in isoform 3. 1 Publication1
Alternative sequenceiVSP_0432111M → MTCNM in isoform 4. Curated1
Alternative sequenceiVSP_0432121M → MTALQLKELSHSGLYRRRRD RPDSLRVNGLPEEELSNM in isoform 5. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS2078.1. [P48059-1]
CCDS54382.1. [P48059-2]
CCDS54383.1. [P48059-4]
CCDS54384.1. [P48059-5]
CCDS54385.1. [P48059-3]
PIRiJC2324.
RefSeqiNP_001180411.1. NM_001193482.1. [P48059-4]
NP_001180412.1. NM_001193483.2. [P48059-2]
NP_001180413.1. NM_001193484.1. [P48059-5]
NP_001180414.1. NM_001193485.2. [P48059-3]
NP_001180417.1. NM_001193488.1. [P48059-1]
NP_004978.2. NM_004987.5. [P48059-1]
UniGeneiHs.597715.
Hs.613268.

Genome annotation databases

EnsembliENST00000332345; ENSP00000331775; ENSG00000169756. [P48059-1]
ENST00000338045; ENSP00000337598; ENSG00000169756. [P48059-3]
ENST00000393310; ENSP00000376987; ENSG00000169756. [P48059-1]
ENST00000409441; ENSP00000387264; ENSG00000169756. [P48059-5]
ENST00000410093; ENSP00000386926; ENSG00000169756. [P48059-4]
ENST00000544547; ENSP00000437912; ENSG00000169756. [P48059-2]
GeneIDi3987.
KEGGihsa:3987.
UCSCiuc002teg.4. human. [P48059-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS2078.1. [P48059-1]
CCDS54382.1. [P48059-2]
CCDS54383.1. [P48059-4]
CCDS54384.1. [P48059-5]
CCDS54385.1. [P48059-3]
PIRiJC2324.
RefSeqiNP_001180411.1. NM_001193482.1. [P48059-4]
NP_001180412.1. NM_001193483.2. [P48059-2]
NP_001180413.1. NM_001193484.1. [P48059-5]
NP_001180414.1. NM_001193485.2. [P48059-3]
NP_001180417.1. NM_001193488.1. [P48059-1]
NP_004978.2. NM_004987.5. [P48059-1]
UniGeneiHs.597715.
Hs.613268.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1G47NMR-A1-70[»]
1NYPNMR-A188-251[»]
1U5SNMR-B188-251[»]
2CORNMR-A125-190[»]
2D8XNMR-A71-127[»]
2KBXNMR-B1-70[»]
3F6QX-ray1.60B6-68[»]
4HI8X-ray1.20B6-68[»]
4HI9X-ray1.20B6-68[»]
ProteinModelPortaliP48059.
SMRiP48059.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi110175. 37 interactors.
DIPiDIP-40671N.
IntActiP48059. 37 interactors.
MINTiMINT-5004275.
STRINGi9606.ENSP00000446121.

PTM databases

iPTMnetiP48059.
PhosphoSitePlusiP48059.

Polymorphism and mutation databases

BioMutaiLIMS1.
DMDMi18266876.

2D gel databases

OGPiP48059.

Proteomic databases

EPDiP48059.
MaxQBiP48059.
PaxDbiP48059.
PeptideAtlasiP48059.
PRIDEiP48059.

Protocols and materials databases

DNASUi3987.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000332345; ENSP00000331775; ENSG00000169756. [P48059-1]
ENST00000338045; ENSP00000337598; ENSG00000169756. [P48059-3]
ENST00000393310; ENSP00000376987; ENSG00000169756. [P48059-1]
ENST00000409441; ENSP00000387264; ENSG00000169756. [P48059-5]
ENST00000410093; ENSP00000386926; ENSG00000169756. [P48059-4]
ENST00000544547; ENSP00000437912; ENSG00000169756. [P48059-2]
GeneIDi3987.
KEGGihsa:3987.
UCSCiuc002teg.4. human. [P48059-1]

Organism-specific databases

CTDi3987.
DisGeNETi3987.
GeneCardsiLIMS1.
HGNCiHGNC:6616. LIMS1.
HPAiHPA058455.
MIMi602567. gene.
neXtProtiNX_P48059.
OpenTargetsiENSG00000169756.
PharmGKBiPA30389.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2272. Eukaryota.
ENOG410XP46. LUCA.
GeneTreeiENSGT00760000118910.
HOGENOMiHOG000253950.
HOVERGENiHBG000053.
InParanoidiP48059.
OMAiHFNCTAC.
OrthoDBiEOG091G08K3.
PhylomeDBiP48059.
TreeFamiTF314113.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000169756-MONOMER.
ReactomeiR-HSA-446353. Cell-extracellular matrix interactions.
R-HSA-446388. Regulation of cytoskeletal remodeling and cell spreading by IPP complex components.

Miscellaneous databases

ChiTaRSiLIMS1. human.
EvolutionaryTraceiP48059.
GeneWikiiLIMS1.
GenomeRNAii3987.
PROiP48059.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000169756.
CleanExiHS_LIMS1.
ExpressionAtlasiP48059. baseline and differential.
GenevisibleiP48059. HS.

Family and domain databases

Gene3Di2.10.110.10. 5 hits.
InterProiIPR017351. PINCH.
IPR001781. Znf_LIM.
[Graphical view]
PANTHERiPTHR24210. PTHR24210. 1 hit.
PfamiPF00412. LIM. 5 hits.
[Graphical view]
PIRSFiPIRSF038003. PINCH. 1 hit.
SMARTiSM00132. LIM. 5 hits.
[Graphical view]
PROSITEiPS00478. LIM_DOMAIN_1. 4 hits.
PS50023. LIM_DOMAIN_2. 5 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiLIMS1_HUMAN
AccessioniPrimary (citable) accession number: P48059
Secondary accession number(s): B2RAJ4
, B7Z483, B7Z7R3, B7Z907, Q53TE0, Q9BS44
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: January 23, 2007
Last modified: November 30, 2016
This is version 174 of the entry and version 4 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

Keywords - Technical termi

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

Documents

  1. Human chromosome 2
    Human chromosome 2: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.