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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: -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

Keywordsi

LigandMetal-binding, Zinc

Enzyme and pathway databases

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

EuPathDBiHostDB:ENSG00000169756.16
HGNCiHGNC:6616 LIMS1
MIMi602567 gene
neXtProtiNX_P48059

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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
ProteomicsDBi55846
55847 [P48059-2]
55848 [P48059-3]
55849 [P48059-4]
55850 [P48059-5]

2D gel databases

OGPiP48059

PTM databases

iPTMnetiP48059
PhosphoSitePlusiP48059

Expressioni

Tissue specificityi

Expressed in most tissues except in the brain.

Gene expression databases

BgeeiENSG00000169756 Expressed in 207 organ(s), highest expression level in endometrium
CleanExiHS_LIMS1
ExpressionAtlasiP48059 baseline and differential
GenevisibleiP48059 HS

Organism-specific databases

HPAiHPA058455
HPA061230

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

GO - Molecular functioni

Protein-protein interaction databases

BioGridi110175, 37 interactors
DIPiDIP-40671N
IntActiP48059, 53 interactors
MINTiP48059
STRINGi9606.ENSP00000446121

Structurei

Secondary structure

1325
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

Keywords - Domaini

LIM domain, Repeat

Phylogenomic databases

eggNOGiKOG2272 Eukaryota
ENOG410XP46 LUCA
GeneTreeiENSGT00760000118910
HOGENOMiHOG000253950
HOVERGENiHBG000053
InParanoidiP48059
OMAiCRECNER
OrthoDBiEOG091G08K3
PhylomeDBiP48059
TreeFamiTF314113

Family and domain databases

InterProiView protein in InterPro
IPR017351 PINCH
IPR001781 Znf_LIM
PANTHERiPTHR24210 PTHR24210, 1 hit
PfamiView protein in Pfam
PF00412 LIM, 5 hits
PIRSFiPIRSF038003 PINCH, 1 hit
SMARTiView protein in SMART
SM00132 LIM, 5 hits
PROSITEiView protein in PROSITE
PS00478 LIM_DOMAIN_1, 4 hits
PS50023 LIM_DOMAIN_2, 5 hits

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

This entry has 5 described isoforms and 5 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 5 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
F8WC86F8WC86_HUMAN
LIM and senescent cell antigen-like...
LIMS1
117Annotation score:
F8WE10F8WE10_HUMAN
LIM and senescent cell antigen-like...
LIMS1
100Annotation score:
C9JF46C9JF46_HUMAN
LIM and senescent cell antigen-like...
LIMS1
176Annotation score:
F8WB59F8WB59_HUMAN
LIM and senescent cell antigen-like...
LIMS1
55Annotation score:
A0A0M3HER1A0A0M3HER1_HUMAN
LIM and senescent cell antigen-like...
LIMS1
209Annotation score:

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

Similar proteinsi

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, 53 interactors
MINTiP48059
STRINGi9606.ENSP00000446121

PTM databases

iPTMnetiP48059
PhosphoSitePlusiP48059

Polymorphism and mutation databases

BioMutaiLIMS1
DMDMi18266876

2D gel databases

OGPiP48059

Proteomic databases

EPDiP48059
MaxQBiP48059
PaxDbiP48059
PeptideAtlasiP48059
PRIDEiP48059
ProteomicsDBi55846
55847 [P48059-2]
55848 [P48059-3]
55849 [P48059-4]
55850 [P48059-5]

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
EuPathDBiHostDB:ENSG00000169756.16
GeneCardsiLIMS1
HGNCiHGNC:6616 LIMS1
HPAiHPA058455
HPA061230
MIMi602567 gene
neXtProtiNX_P48059
OpenTargetsiENSG00000169756
PharmGKBiPA30389
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2272 Eukaryota
ENOG410XP46 LUCA
GeneTreeiENSGT00760000118910
HOGENOMiHOG000253950
HOVERGENiHBG000053
InParanoidiP48059
OMAiCRECNER
OrthoDBiEOG091G08K3
PhylomeDBiP48059
TreeFamiTF314113

Enzyme and pathway databases

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
PROiPR:P48059
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000169756 Expressed in 207 organ(s), highest expression level in endometrium
CleanExiHS_LIMS1
ExpressionAtlasiP48059 baseline and differential
GenevisibleiP48059 HS

Family and domain databases

InterProiView protein in InterPro
IPR017351 PINCH
IPR001781 Znf_LIM
PANTHERiPTHR24210 PTHR24210, 1 hit
PfamiView protein in Pfam
PF00412 LIM, 5 hits
PIRSFiPIRSF038003 PINCH, 1 hit
SMARTiView protein in SMART
SM00132 LIM, 5 hits
PROSITEiView protein in PROSITE
PS00478 LIM_DOMAIN_1, 4 hits
PS50023 LIM_DOMAIN_2, 5 hits
ProtoNetiSearch...

Entry informationi

Entry nameiLIMS1_HUMAN
AccessioniPrimary (citable) accession number: P48059
Secondary accession number(s): B2RAJ4
, B7Z483, B7Z7R3, B7Z907, Q53TE0, Q9BS44
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: January 23, 2007
Last modified: September 12, 2018
This is version 188 of the entry and version 4 of the sequence. See 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
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