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Protein

LIM domain-binding protein 1

Gene

Ldb1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Binds to the LIM domain of a wide variety of LIM domain-containing transcription factors. May regulate the transcriptional activity of LIM-containing proteins by determining specific partner interactions. Plays a role in the development of interneurons and motor neurons in cooperation with LHX3 and ISL1. Acts synergistically with LHX1/LIM1 in axis formation and activation of gene expression. Acts with LMO2 in the regulation of red blood cell development, maintaining erythroid precursors in an immature state.7 Publications

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDevelopmental protein

Enzyme and pathway databases

ReactomeiR-MMU-8939236 RUNX1 regulates transcription of genes involved in differentiation of HSCs

Names & Taxonomyi

Protein namesi
Recommended name:
LIM domain-binding protein 1
Short name:
LDB-1
Alternative name(s):
Carboxyl-terminal LIM domain-binding protein 2
Short name:
CLIM-2
LIM domain-binding factor CLIM2
Short name:
mLdb1
Nuclear LIM interactor
Gene namesi
Name:Ldb1
Synonyms:Nli
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 19

Organism-specific databases

MGIiMGI:894762 Ldb1

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

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00000843852 – 411LIM domain-binding protein 1Add BLAST410

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineBy similarity1
Modified residuei61PhosphothreonineCombined sources1
Modified residuei265PhosphoserineBy similarity1
Modified residuei302PhosphoserineCombined sources1

Post-translational modificationi

Ubiquitinated by RLIM/RNF12, leading to its degradation by the proteasome.1 Publication

Keywords - PTMi

Acetylation, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP70662
PaxDbiP70662
PRIDEiP70662

PTM databases

iPTMnetiP70662
PhosphoSitePlusiP70662

Expressioni

Tissue specificityi

Expression overlaps that of LIM domain-containing proteins. Expressed widely in the embryo with highest expression in several regions of the brain the central nervous system ganglia. Also expressed in fetal liver, lung, kidney, thymus and olfactory epithelium. Expressed in multiple adult tissues including heart, brain, liver, kidney, testis, lung and muscle and a diverse range of neuronal cell types, with expression highest in the pituitary gland and skin. Expressed in both embryonic and adult hemopoietic cells, including the erythroid lineage.4 Publications

Gene expression databases

BgeeiENSMUSG00000025223 Expressed in 300 organ(s), highest expression level in cerebral cortex
CleanExiMM_LDB1
ExpressionAtlasiP70662 baseline and differential
GenevisibleiP70662 MM

Interactioni

Subunit structurei

Interacts with ESR1 (By similarity). Forms homodimers and heterodimers. Interacts with and activates LHX1/LIM1. Interacts with the LIM domains of ISL1 and LMO2. Can assemble in a complex with LMO2 and TAL1/SCL but does not interact with TAL1/SCL directly. Strongly interacts with the LIM2 domain of LMX1A and more weakly with the LIM1 domain. Homodimerization is not required for, and does not effect, LMX1A-binding. Component of a nuclear TAL-1 complex composed at least of CBFA2T3, LDB1, TAL1 and TCF3. Interacts with LHX6 and LHX9. At neuronal promoters, forms a complex with LHX3 involved in the specification of interneurons, in motor neurons, it is displaced by ISL1 to form a ternary complex in which ISL1 contacts both LHX3 and LDB1. Interacts with SLK; leading to negatively regulate SLK kinase activity (PubMed:19675209).By similarity11 Publications

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi201125, 29 interactors
CORUMiP70662
DIPiDIP-42842N
IntActiP70662, 7 interactors
MINTiP70662
STRINGi10090.ENSMUSP00000118546

Structurei

Secondary structure

1411
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP70662
SMRiP70662
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP70662

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni336 – 374LIM-binding domain (LID)Add BLAST39

Domaini

The dimerization domain is located in the N-terminus.1 Publication

Sequence similaritiesi

Belongs to the LDB family.Curated

Phylogenomic databases

eggNOGiKOG2181 Eukaryota
ENOG410YZVH LUCA
GeneTreeiENSGT00390000005639
HOGENOMiHOG000030908
HOVERGENiHBG000135
InParanoidiP70662
KOiK15617
OrthoDBiEOG091G0A0P
PhylomeDBiP70662
TreeFamiTF319923

Family and domain databases

InterProiView protein in InterPro
IPR030167 LDB1
IPR029005 LIM-bd/SEUSS
PANTHERiPTHR10378 PTHR10378, 1 hit
PTHR10378:SF7 PTHR10378:SF7, 1 hit
PfamiView protein in Pfam
PF01803 LIM_bind, 2 hits

Sequences (3+)i

Sequence statusi: Complete.

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

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 3 described isoforms and 1 potential isoform that is computationally mapped.Show allAlign All

Isoform 1 (identifier: P70662-1) [UniParc]FASTAAdd to basket
Also known as: Visvader-a

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
MSVGCACPGC SSKSFKLYSP KEPPNGNAFP PFHPGTMLDR DVGPTPMYPP
60 70 80 90 100
TYLEPGIGRH TPYGNQTDYR IFELNKRLQN WTEECDNLWW DAFTTEFFED
110 120 130 140 150
DAMLTITFCL EDGPKRYTIG RTLIPRYFRS IFEGGATELY YVLKHPKEAF
160 170 180 190 200
HSNFVSLDCD QGSMVTQHGK PMFTQVCVEG RLYLEFMFDD MMRIKTWHFS
210 220 230 240 250
IRQHRELIPR SILAMHAQDP QMLDQLSKNI TRCGLSNSTL NYLRLCVILE
260 270 280 290 300
PMQELMSRHK TYSLSPRDCL KTCLFQKWQR MVAPPAEPAR QQPSKRRKRK
310 320 330 340 350
MSGGSTMSSG GGNTNNSNSK KKSPASTFAL SSQVPDVMVV GEPTLMGGEF
360 370 380 390 400
GDEDERLITR LENTQFDAAN GIDDEDSFNN SPALGANSPW NSKPPSSQES
410
KSENPTSQAS Q
Length:411
Mass (Da):46,503
Last modified:September 11, 2007 - v2
Checksum:i47C53DFA23044580
GO
Isoform 2 (identifier: P70662-2) [UniParc]FASTAAdd to basket
Also known as: Tran-b

The sequence of this isoform differs from the canonical sequence as follows:
     1-36: Missing.
     336-355: DVMVVGEPTLMGGEFGDEDE → VSISAFFSSGLPHCSPLTPV
     356-411: Missing.

Note: Due to intron retention. Lacks LIM-binding domain. Lacks ability to activate LIM domain-dependent transcription.
Show »
Length:319
Mass (Da):36,667
Checksum:i2FD1D15303732E5E
GO
Isoform 3 (identifier: P70662-3) [UniParc]FASTAAdd to basket
Also known as: Tran-a

The sequence of this isoform differs from the canonical sequence as follows:
     1-36: Missing.

Show »
Length:375
Mass (Da):42,779
Checksum:i75FACF0CA0BD2DE7
GO

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
D3Z1C5D3Z1C5_MOUSE
LIM domain-binding protein 1
Ldb1
373Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti262Y → C in AAB96885 (PubMed:9192866).Curated1
Sequence conflicti334V → A in AAB96885 (PubMed:9192866).Curated1
Sequence conflicti389 – 390PW → QR in AAB96885 (PubMed:9192866).Curated2

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0278331 – 36Missing in isoform 2 and isoform 3. 5 PublicationsAdd BLAST36
Alternative sequenceiVSP_027834336 – 355DVMVV…GDEDE → VSISAFFSSGLPHCSPLTPV in isoform 2. 1 PublicationAdd BLAST20
Alternative sequenceiVSP_027835356 – 411Missing in isoform 2. 1 PublicationAdd BLAST56

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U70375 mRNA Translation: AAC52933.1
U69270 mRNA Translation: AAC52887.1
U89488 mRNA Translation: AAB96885.1
AF030333 mRNA Translation: AAB94131.1
AF024524 Genomic DNA Translation: AAC40064.1
AB250383 mRNA Translation: BAE95401.1
BC013624 mRNA Translation: AAH13624.1
CCDSiCCDS29870.1 [P70662-3]
CCDS50455.1 [P70662-1]
RefSeqiNP_001106879.1, NM_001113408.1 [P70662-1]
NP_034827.1, NM_010697.1 [P70662-3]
XP_011245459.1, XM_011247157.1
UniGeneiMm.327442

Genome annotation databases

EnsembliENSMUST00000026252; ENSMUSP00000026252; ENSMUSG00000025223 [P70662-3]
ENSMUST00000056931; ENSMUSP00000053680; ENSMUSG00000025223 [P70662-3]
ENSMUST00000137771; ENSMUSP00000114667; ENSMUSG00000025223 [P70662-2]
ENSMUST00000156585; ENSMUSP00000118546; ENSMUSG00000025223 [P70662-1]
ENSMUST00000185355; ENSMUSP00000139562; ENSMUSG00000025223 [P70662-1]
GeneIDi16825
KEGGimmu:16825
UCSCiuc008hrz.1 mouse [P70662-1]
uc008hsa.1 mouse [P70662-2]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U70375 mRNA Translation: AAC52933.1
U69270 mRNA Translation: AAC52887.1
U89488 mRNA Translation: AAB96885.1
AF030333 mRNA Translation: AAB94131.1
AF024524 Genomic DNA Translation: AAC40064.1
AB250383 mRNA Translation: BAE95401.1
BC013624 mRNA Translation: AAH13624.1
CCDSiCCDS29870.1 [P70662-3]
CCDS50455.1 [P70662-1]
RefSeqiNP_001106879.1, NM_001113408.1 [P70662-1]
NP_034827.1, NM_010697.1 [P70662-3]
XP_011245459.1, XM_011247157.1
UniGeneiMm.327442

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1J2ONMR-A336-375[»]
1M3VNMR-A336-375[»]
1RUTX-ray1.30X336-375[»]
2JTNNMR-A331-375[»]
2L6YNMR-B336-348[»]
2L6ZNMR-C336-348[»]
2LXDNMR-A336-375[»]
4JCJX-ray3.00A/B/C336-366[»]
ProteinModelPortaliP70662
SMRiP70662
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi201125, 29 interactors
CORUMiP70662
DIPiDIP-42842N
IntActiP70662, 7 interactors
MINTiP70662
STRINGi10090.ENSMUSP00000118546

PTM databases

iPTMnetiP70662
PhosphoSitePlusiP70662

Proteomic databases

MaxQBiP70662
PaxDbiP70662
PRIDEiP70662

Protocols and materials databases

DNASUi16825
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000026252; ENSMUSP00000026252; ENSMUSG00000025223 [P70662-3]
ENSMUST00000056931; ENSMUSP00000053680; ENSMUSG00000025223 [P70662-3]
ENSMUST00000137771; ENSMUSP00000114667; ENSMUSG00000025223 [P70662-2]
ENSMUST00000156585; ENSMUSP00000118546; ENSMUSG00000025223 [P70662-1]
ENSMUST00000185355; ENSMUSP00000139562; ENSMUSG00000025223 [P70662-1]
GeneIDi16825
KEGGimmu:16825
UCSCiuc008hrz.1 mouse [P70662-1]
uc008hsa.1 mouse [P70662-2]

Organism-specific databases

CTDi8861
MGIiMGI:894762 Ldb1

Phylogenomic databases

eggNOGiKOG2181 Eukaryota
ENOG410YZVH LUCA
GeneTreeiENSGT00390000005639
HOGENOMiHOG000030908
HOVERGENiHBG000135
InParanoidiP70662
KOiK15617
OrthoDBiEOG091G0A0P
PhylomeDBiP70662
TreeFamiTF319923

Enzyme and pathway databases

ReactomeiR-MMU-8939236 RUNX1 regulates transcription of genes involved in differentiation of HSCs

Miscellaneous databases

ChiTaRSiLdb1 mouse
EvolutionaryTraceiP70662
PROiPR:P70662
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000025223 Expressed in 300 organ(s), highest expression level in cerebral cortex
CleanExiMM_LDB1
ExpressionAtlasiP70662 baseline and differential
GenevisibleiP70662 MM

Family and domain databases

InterProiView protein in InterPro
IPR030167 LDB1
IPR029005 LIM-bd/SEUSS
PANTHERiPTHR10378 PTHR10378, 1 hit
PTHR10378:SF7 PTHR10378:SF7, 1 hit
PfamiView protein in Pfam
PF01803 LIM_bind, 2 hits
ProtoNetiSearch...

Entry informationi

Entry nameiLDB1_MOUSE
AccessioniPrimary (citable) accession number: P70662
Secondary accession number(s): O55204, Q1EQX2, Q71V68
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: September 11, 2007
Last modified: November 7, 2018
This is version 158 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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