UniProtKB - P70662 (LDB1_MOUSE)
LIM domain-binding protein 1
Ldb1
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 PublicationsGO - Molecular functioni
- chromatin binding Source: MGI
- DNA-binding transcription factor binding Source: MGI
- enzyme binding Source: UniProtKB
- identical protein binding Source: MGI
- LIM domain binding Source: UniProtKB
- protein homodimerization activity Source: UniProtKB
- protein self-association Source: MGI
- RNA polymerase II-specific DNA-binding transcription factor binding Source: MGI
- transcription coregulator activity Source: InterPro
GO - Biological processi
- anterior/posterior axis specification Source: MGI
- cell differentiation Source: MGI
- cellular component assembly Source: MGI
- cerebellar Purkinje cell differentiation Source: MGI
- cerebellum development Source: MGI
- epithelial structure maintenance Source: MGI
- gastrulation with mouth forming second Source: MGI
- hair follicle development Source: MGI
- head development Source: UniProtKB
- histone H3-K4 acetylation Source: BHF-UCL
- mesendoderm development Source: MGI
- negative regulation of erythrocyte differentiation Source: UniProtKB
- negative regulation of transcription, DNA-templated Source: MGI
- negative regulation of transcription by RNA polymerase II Source: GO_Central
- nervous system development Source: GO_Central
- neuron differentiation Source: UniProtKB
- positive regulation of cell adhesion Source: MGI
- positive regulation of hemoglobin biosynthetic process Source: BHF-UCL
- positive regulation of transcription by RNA polymerase II Source: BHF-UCL
- primitive erythrocyte differentiation Source: BHF-UCL
- regulation of cell migration Source: UniProtKB
- regulation of focal adhesion assembly Source: UniProtKB
- regulation of kinase activity Source: UniProtKB
- regulation of transcription elongation from RNA polymerase II promoter Source: BHF-UCL
- somatic stem cell population maintenance Source: MGI
- transcription by RNA polymerase II Source: UniProtKB
- transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery Source: BHF-UCL
- Wnt signaling pathway Source: MGI
Keywordsi
Molecular function | Developmental protein |
Enzyme and pathway databases
Reactomei | R-MMU-8939236, RUNX1 regulates transcription of genes involved in differentiation of HSCs |
Names & Taxonomyi
Protein namesi | Recommended name: LIM domain-binding protein 1Short 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 |
Organismi | Mus musculus (Mouse) |
Taxonomic identifieri | 10090 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Myomorpha › Muroidea › Muridae › Murinae › Mus › Mus |
Proteomesi |
|
Organism-specific databases
MGIi | MGI:894762, Ldb1 |
VEuPathDBi | HostDB:ENSMUSG00000025223 |
Subcellular locationi
Nucleus
- beta-catenin-TCF complex Source: MGI
- nucleoplasm Source: Reactome
- nucleus Source: UniProtKB
- RNA polymerase II transcription regulator complex Source: MGI
Other locations
- cell leading edge Source: UniProtKB
- chromatin Source: MGI
- protein-containing complex Source: UniProtKB
- transcription regulator complex Source: MGI
Keywords - Cellular componenti
NucleusPTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Initiator methioninei | RemovedBy similarity | |||
ChainiPRO_0000084385 | 2 – 411 | LIM domain-binding protein 1Add BLAST | 410 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Modified residuei | 2 | N-acetylserineBy similarity | 1 | |
Modified residuei | 61 | PhosphothreonineCombined sources | 1 | |
Modified residuei | 265 | PhosphoserineBy similarity | 1 | |
Modified residuei | 302 | PhosphoserineCombined sources | 1 |
Post-translational modificationi
Keywords - PTMi
Acetylation, Phosphoprotein, Ubl conjugationProteomic databases
EPDi | P70662 |
MaxQBi | P70662 |
PaxDbi | P70662 |
PRIDEi | P70662 |
ProteomicsDBi | 264922 [P70662-1] 264923 [P70662-2] 264924 [P70662-3] |
PTM databases
iPTMneti | P70662 |
PhosphoSitePlusi | P70662 |
Expressioni
Tissue specificityi
Gene expression databases
Bgeei | ENSMUSG00000025223, Expressed in brain and 320 other tissues |
ExpressionAtlasi | P70662, baseline and differential |
Genevisiblei | P70662, 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).
Interacts with YWHAZ (By similarity).
Interacts with PRDM1/BLIMP1 (By similarity).
By similarity11 PublicationsBinary interactionsi
P70662
GO - Molecular functioni
- DNA-binding transcription factor binding Source: MGI
- enzyme binding Source: UniProtKB
- identical protein binding Source: MGI
- LIM domain binding Source: UniProtKB
- protein homodimerization activity Source: UniProtKB
- protein self-association Source: MGI
- RNA polymerase II-specific DNA-binding transcription factor binding Source: MGI
Protein-protein interaction databases
BioGRIDi | 201125, 31 interactors |
CORUMi | P70662 |
DIPi | DIP-42842N |
IntActi | P70662, 30 interactors |
MINTi | P70662 |
STRINGi | 10090.ENSMUSP00000118546 |
Miscellaneous databases
RNActi | P70662, protein |
Structurei
Secondary structure
3D structure databases
AlphaFoldDBi | P70662 |
SASBDBi | P70662 |
SMRi | P70662 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | P70662 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 336 – 375 | LIM interaction domain (LID)PROSITE-ProRule annotationAdd BLAST | 40 |
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 284 – 330 | DisorderedSequence analysisAdd BLAST | 47 | |
Regioni | 367 – 411 | DisorderedSequence analysisAdd BLAST | 45 |
Compositional bias
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Compositional biasi | 303 – 330 | Polar residuesSequence analysisAdd BLAST | 28 | |
Compositional biasi | 374 – 411 | Polar residuesSequence analysisAdd BLAST | 38 |
Domaini
Sequence similaritiesi
Phylogenomic databases
eggNOGi | KOG2181, Eukaryota |
GeneTreei | ENSGT00390000005639 |
HOGENOMi | CLU_032597_0_0_1 |
InParanoidi | P70662 |
OrthoDBi | 849287at2759 |
PhylomeDBi | P70662 |
TreeFami | TF319923 |
Family and domain databases
IDEALi | IID50049 |
InterProi | View protein in InterPro IPR030167, LDB1 IPR041363, LID IPR029005, LIM-bd/SEUSS |
PANTHERi | PTHR10378, PTHR10378, 1 hit PTHR10378:SF7, PTHR10378:SF7, 1 hit |
Pfami | View protein in Pfam PF17916, LID, 1 hit PF01803, LIM_bind, 2 hits |
PROSITEi | View protein in PROSITE PS51957, LID, 1 hit |
s (3+)i Sequence
Sequence statusi: Complete.
: The displayed sequence is further processed into a mature form. Sequence processingi
This entry describes 3 produced by isoformsialternative splicing. AlignAdd to basketThis entry has 3 described isoforms and 1 potential isoform that is computationally mapped.Show allAlign All
This isoform has been chosen as the sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry. canonicali
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
The sequence of this isoform differs from the canonical sequence as follows:
1-36: Missing.
336-355: DVMVVGEPTLMGGEFGDEDE → VSISAFFSSGLPHCSPLTPV
356-411: Missing.
Computationally mapped potential isoform sequencesi
There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basketD3Z1C5 | D3Z1C5_MOUSE | LIM domain-binding protein 1 | Ldb1 | 373 | Annotation score: |
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 262 | Y → C in AAB96885 (PubMed:9192866).Curated | 1 | |
Sequence conflicti | 334 | V → A in AAB96885 (PubMed:9192866).Curated | 1 | |
Sequence conflicti | 389 – 390 | PW → QR in AAB96885 (PubMed:9192866).Curated | 2 |
Alternative sequence
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Alternative sequenceiVSP_027833 | 1 – 36 | Missing in isoform 2 and isoform 3. 5 PublicationsAdd BLAST | 36 | |
Alternative sequenceiVSP_027834 | 336 – 355 | DVMVV…GDEDE → VSISAFFSSGLPHCSPLTPV in isoform 2. 1 PublicationAdd BLAST | 20 | |
Alternative sequenceiVSP_027835 | 356 – 411 | Missing in isoform 2. 1 PublicationAdd BLAST | 56 |
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 |
CCDSi | CCDS29870.1 [P70662-3] CCDS50455.1 [P70662-1] |
RefSeqi | NP_001106879.1, NM_001113408.1 [P70662-1] NP_034827.1, NM_010697.1 [P70662-3] XP_011245459.1, XM_011247157.1 |
Genome annotation databases
Ensembli | ENSMUST00000026252; ENSMUSP00000026252; ENSMUSG00000025223 [P70662-3] ENSMUST00000056931; ENSMUSP00000053680; ENSMUSG00000025223 [P70662-3] ENSMUST00000137771; ENSMUSP00000114667; ENSMUSG00000025223 [P70662-2] ENSMUST00000156585; ENSMUSP00000118546; ENSMUSG00000025223 [P70662-1] ENSMUST00000185355; ENSMUSP00000139562; ENSMUSG00000025223 [P70662-1] |
GeneIDi | 16825 |
KEGGi | mmu:16825 |
UCSCi | uc008hrz.1, mouse [P70662-1] uc008hsa.1, mouse [P70662-2] |
Keywords - Coding sequence diversityi
Alternative splicingSimilar 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 |
CCDSi | CCDS29870.1 [P70662-3] CCDS50455.1 [P70662-1] |
RefSeqi | NP_001106879.1, NM_001113408.1 [P70662-1] NP_034827.1, NM_010697.1 [P70662-3] XP_011245459.1, XM_011247157.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
1J2O | NMR | - | A | 336-375 | [»] | |
1M3V | NMR | - | A | 336-375 | [»] | |
1RUT | X-ray | 1.30 | X | 336-375 | [»] | |
2JTN | NMR | - | A | 331-375 | [»] | |
2L6Y | NMR | - | B | 336-348 | [»] | |
2L6Z | NMR | - | C | 336-348 | [»] | |
2LXD | NMR | - | A | 336-375 | [»] | |
4JCJ | X-ray | 3.00 | A/B/C | 336-366 | [»] | |
6PTL | X-ray | 2.50 | A | 50-236 | [»] | |
AlphaFoldDBi | P70662 | |||||
SASBDBi | P70662 | |||||
SMRi | P70662 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 201125, 31 interactors |
CORUMi | P70662 |
DIPi | DIP-42842N |
IntActi | P70662, 30 interactors |
MINTi | P70662 |
STRINGi | 10090.ENSMUSP00000118546 |
PTM databases
iPTMneti | P70662 |
PhosphoSitePlusi | P70662 |
Proteomic databases
EPDi | P70662 |
MaxQBi | P70662 |
PaxDbi | P70662 |
PRIDEi | P70662 |
ProteomicsDBi | 264922 [P70662-1] 264923 [P70662-2] 264924 [P70662-3] |
Protocols and materials databases
Antibodypediai | 17969, 277 antibodies from 30 providers |
DNASUi | 16825 |
Genome annotation databases
Ensembli | ENSMUST00000026252; ENSMUSP00000026252; ENSMUSG00000025223 [P70662-3] ENSMUST00000056931; ENSMUSP00000053680; ENSMUSG00000025223 [P70662-3] ENSMUST00000137771; ENSMUSP00000114667; ENSMUSG00000025223 [P70662-2] ENSMUST00000156585; ENSMUSP00000118546; ENSMUSG00000025223 [P70662-1] ENSMUST00000185355; ENSMUSP00000139562; ENSMUSG00000025223 [P70662-1] |
GeneIDi | 16825 |
KEGGi | mmu:16825 |
UCSCi | uc008hrz.1, mouse [P70662-1] uc008hsa.1, mouse [P70662-2] |
Organism-specific databases
CTDi | 8861 |
MGIi | MGI:894762, Ldb1 |
VEuPathDBi | HostDB:ENSMUSG00000025223 |
Phylogenomic databases
eggNOGi | KOG2181, Eukaryota |
GeneTreei | ENSGT00390000005639 |
HOGENOMi | CLU_032597_0_0_1 |
InParanoidi | P70662 |
OrthoDBi | 849287at2759 |
PhylomeDBi | P70662 |
TreeFami | TF319923 |
Enzyme and pathway databases
Reactomei | R-MMU-8939236, RUNX1 regulates transcription of genes involved in differentiation of HSCs |
Miscellaneous databases
BioGRID-ORCSi | 16825, 8 hits in 73 CRISPR screens |
ChiTaRSi | Ldb1, mouse |
EvolutionaryTracei | P70662 |
PROi | PR:P70662 |
RNActi | P70662, protein |
SOURCEi | Search... |
Gene expression databases
Bgeei | ENSMUSG00000025223, Expressed in brain and 320 other tissues |
ExpressionAtlasi | P70662, baseline and differential |
Genevisiblei | P70662, MM |
Family and domain databases
IDEALi | IID50049 |
InterProi | View protein in InterPro IPR030167, LDB1 IPR041363, LID IPR029005, LIM-bd/SEUSS |
PANTHERi | PTHR10378, PTHR10378, 1 hit PTHR10378:SF7, PTHR10378:SF7, 1 hit |
Pfami | View protein in Pfam PF17916, LID, 1 hit PF01803, LIM_bind, 2 hits |
PROSITEi | View protein in PROSITE PS51957, LID, 1 hit |
MobiDBi | Search... |
Entry informationi
Entry namei | LDB1_MOUSE | |
Accessioni | P70662Primary (citable) accession number: P70662 Secondary accession number(s): O55204, Q1EQX2, Q71V68 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | July 15, 1998 |
Last sequence update: | September 11, 2007 | |
Last modified: | May 25, 2022 | |
This is version 177 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- MGD cross-references
Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families