UniProtKB - Q86U70 (LDB1_HUMAN)
LIM domain-binding protein 1
LDB1
Functioni
Miscellaneous
GO - Molecular functioni
- DNA-binding transcription factor binding Source: UniProtKB
- enzyme binding Source: UniProtKB
- LIM domain binding Source: UniProtKB
- protein homodimerization activity Source: UniProtKB
- RNA polymerase II activating transcription factor binding Source: BHF-UCL
- transcription coregulator activity Source: InterPro
GO - Biological processi
- histone H3-K4 acetylation Source: BHF-UCL
- multicellular organism development Source: UniProtKB
- negative regulation of erythrocyte differentiation Source: UniProtKB
- negative regulation of transcription, DNA-templated Source: UniProtKB
- negative regulation of transcription by RNA polymerase II Source: GO_Central
- nervous system development Source: GO_Central
- neuron differentiation Source: UniProtKB
- positive regulation of hemoglobin biosynthetic process Source: BHF-UCL
- positive regulation of transcription by RNA polymerase II Source: BHF-UCL
- regulation of cell migration Source: UniProtKB
- regulation of focal adhesion assembly Source: UniProtKB
- regulation of hematopoietic stem cell differentiation Source: Reactome
- regulation of kinase activity Source: UniProtKB
- regulation of transcription, DNA-templated Source: ProtInc
- regulation of transcription elongation from RNA polymerase II promoter Source: BHF-UCL
- transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery Source: BHF-UCL
Keywordsi
Molecular function | Developmental protein |
Enzyme and pathway databases
PathwayCommonsi | Q86U70 |
Reactomei | R-HSA-8939236, RUNX1 regulates transcription of genes involved in differentiation of HSCs R-HSA-9010553, Regulation of expression of SLITs and ROBOs |
SIGNORi | Q86U70 |
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: hLdb1 Nuclear LIM interactor |
Gene namesi | Name:LDB1 Synonyms:CLIM2 |
Organismi | Homo sapiens (Human) |
Taxonomic identifieri | 9606 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Proteomesi |
|
Organism-specific databases
EuPathDBi | HostDB:ENSG00000198728.10 |
HGNCi | HGNC:6532, LDB1 |
MIMi | 603451, gene |
neXtProti | NX_Q86U70 |
Subcellular locationi
Nucleus
- Nucleus Curated
Nucleus
- nuclear chromatin Source: BHF-UCL
- nucleoplasm Source: Reactome
- nucleus Source: UniProtKB
Other locations
- beta-catenin-TCF complex Source: FlyBase
- cell leading edge Source: UniProtKB
- protein-containing complex Source: UniProtKB
- transcription regulator complex Source: BHF-UCL
Keywords - Cellular componenti
NucleusPathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 245 – 249 | LCVIL → ACVAA: Abolishes interaction with ESR1. 1 Publication | 5 |
Organism-specific databases
DisGeNETi | 8861 |
OpenTargetsi | ENSG00000198728 |
PharmGKBi | PA30316 |
Miscellaneous databases
Pharosi | Q86U70, Tbio |
Polymorphism and mutation databases
BioMutai | LDB1 |
DMDMi | 158518615 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Initiator methioninei | RemovedCombined sources | |||
ChainiPRO_0000084384 | 2 – 411 | LIM domain-binding protein 1Add BLAST | 410 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Modified residuei | 2 | N-acetylserineCombined sources | 1 | |
Modified residuei | 61 | PhosphothreonineBy similarity | 1 | |
Modified residuei | 265 | PhosphoserineCombined sources | 1 | |
Modified residuei | 302 | PhosphoserineBy similarity | 1 |
Post-translational modificationi
Keywords - PTMi
Acetylation, Phosphoprotein, Ubl conjugationProteomic databases
EPDi | Q86U70 |
jPOSTi | Q86U70 |
MassIVEi | Q86U70 |
MaxQBi | Q86U70 |
PaxDbi | Q86U70 |
PeptideAtlasi | Q86U70 |
PRIDEi | Q86U70 |
ProteomicsDBi | 69771 [Q86U70-1] 69772 [Q86U70-2] 69773 [Q86U70-3] |
PTM databases
iPTMneti | Q86U70 |
PhosphoSitePlusi | Q86U70 |
Expressioni
Tissue specificityi
Gene expression databases
Bgeei | ENSG00000198728, Expressed in right ovary and 201 other tissues |
Genevisiblei | Q86U70, HS |
Organism-specific databases
HPAi | ENSG00000198728, Low tissue specificity |
Interactioni
Subunit structurei
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 (By similarity).
Interacts with ESR1.
Interacts with SLK; leading to negatively regulate SLK kinase activity (By similarity).
Interacts with YWHAZ (PubMed:16959763).
Interacts with PRDM1/BLIMP1 (PubMed:32417234).
By similarity4 PublicationsBinary interactionsi
Hide detailsQ86U70
Isoform 3 [Q86U70-2]
GO - Molecular functioni
- DNA-binding transcription factor binding Source: UniProtKB
- enzyme binding Source: UniProtKB
- LIM domain binding Source: UniProtKB
- protein homodimerization activity Source: UniProtKB
- RNA polymerase II activating transcription factor binding Source: BHF-UCL
Protein-protein interaction databases
BioGRIDi | 114384, 52 interactors |
CORUMi | Q86U70 |
DIPi | DIP-31826N |
IntActi | Q86U70, 37 interactors |
MINTi | Q86U70 |
STRINGi | 9606.ENSP00000392466 |
Miscellaneous databases
RNActi | Q86U70, protein |
Structurei
Secondary structure
3D structure databases
SMRi | Q86U70 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | Q86U70 |
Family & Domainsi
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 336 – 374 | LIM-binding domain (LID)By similarityAdd BLAST | 39 |
Domaini
Sequence similaritiesi
Phylogenomic databases
eggNOGi | KOG2181, Eukaryota |
GeneTreei | ENSGT00390000005639 |
HOGENOMi | CLU_032597_0_0_1 |
InParanoidi | Q86U70 |
OMAi | KMSVGCA |
OrthoDBi | 849287at2759 |
PhylomeDBi | Q86U70 |
TreeFami | TF319923 |
Family and domain databases
IDEALi | IID00282 |
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 |
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 MVAPPAEPTR 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.
336-352: DVMVVGEPTLMGGEFGD → VSISAFFSLLGCPTTHP
353-411: Missing.
Computationally mapped potential isoform sequencesi
There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basketA0A6E1WJ75 | A0A6E1WJ75_HUMAN | LIM domain binding 1, isoform CRA_c | LDB1 hCG_25635 | 409 | Annotation score: |
Sequence cautioni
Natural variant
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Natural variantiVAR_036366 | 299 | R → Q in a colorectal cancer sample; somatic mutation. 1 PublicationCorresponds to variant dbSNP:rs990101456Ensembl. | 1 |
Alternative sequence
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Alternative sequenceiVSP_027830 | 1 – 36 | Missing in isoform 2 and isoform 3. 7 PublicationsAdd BLAST | 36 | |
Alternative sequenceiVSP_027831 | 336 – 352 | DVMVV…GEFGD → VSISAFFSLLGCPTTHP in isoform 2. 2 PublicationsAdd BLAST | 17 | |
Alternative sequenceiVSP_027832 | 353 – 411 | Missing in isoform 2. 2 PublicationsAdd BLAST | 59 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AF068652 mRNA Translation: AAC77818.1 AJ243098 Genomic DNA Translation: CAB45409.1 Different initiation. AB016485 mRNA Translation: BAA31991.1 AB250384 mRNA Translation: BAE95402.1 AF064491 mRNA Translation: AAC28341.1 BT007054 mRNA Translation: AAP35703.1 AK300588 mRNA Translation: BAG62286.1 AL500527 Genomic DNA No translation available. BC000482 mRNA Translation: AAH00482.1 BC009246 mRNA Translation: AAH09246.1 |
CCDSi | CCDS44472.1 [Q86U70-1] CCDS7528.1 [Q86U70-2] |
RefSeqi | NP_001106878.1, NM_001113407.2 [Q86U70-1] NP_003884.1, NM_003893.4 [Q86U70-2] |
Genome annotation databases
Ensembli | ENST00000361198; ENSP00000354616; ENSG00000198728 [Q86U70-2] ENST00000673968; ENSP00000501277; ENSG00000198728 [Q86U70-1] |
GeneIDi | 8861 |
KEGGi | hsa:8861 |
UCSCi | uc001kuk.6, human [Q86U70-1] |
Keywords - Coding sequence diversityi
Alternative splicing, PolymorphismSimilar proteinsi
Cross-referencesi
Web resourcesi
Atlas of Genetics and Cytogenetics in Oncology and Haematology |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AF068652 mRNA Translation: AAC77818.1 AJ243098 Genomic DNA Translation: CAB45409.1 Different initiation. AB016485 mRNA Translation: BAA31991.1 AB250384 mRNA Translation: BAE95402.1 AF064491 mRNA Translation: AAC28341.1 BT007054 mRNA Translation: AAP35703.1 AK300588 mRNA Translation: BAG62286.1 AL500527 Genomic DNA No translation available. BC000482 mRNA Translation: AAH00482.1 BC009246 mRNA Translation: AAH09246.1 |
CCDSi | CCDS44472.1 [Q86U70-1] CCDS7528.1 [Q86U70-2] |
RefSeqi | NP_001106878.1, NM_001113407.2 [Q86U70-1] NP_003884.1, NM_003893.4 [Q86U70-2] |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
2XJY | X-ray | 2.40 | B | 334-368 | [»] | |
2XJZ | X-ray | 2.80 | I/J/K/L/M | 334-368 | [»] | |
2YPA | X-ray | 2.80 | D | 336-375 | [»] | |
6TYD | X-ray | 2.80 | V | 56-285 | [»] | |
SMRi | Q86U70 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 114384, 52 interactors |
CORUMi | Q86U70 |
DIPi | DIP-31826N |
IntActi | Q86U70, 37 interactors |
MINTi | Q86U70 |
STRINGi | 9606.ENSP00000392466 |
PTM databases
iPTMneti | Q86U70 |
PhosphoSitePlusi | Q86U70 |
Polymorphism and mutation databases
BioMutai | LDB1 |
DMDMi | 158518615 |
Proteomic databases
EPDi | Q86U70 |
jPOSTi | Q86U70 |
MassIVEi | Q86U70 |
MaxQBi | Q86U70 |
PaxDbi | Q86U70 |
PeptideAtlasi | Q86U70 |
PRIDEi | Q86U70 |
ProteomicsDBi | 69771 [Q86U70-1] 69772 [Q86U70-2] 69773 [Q86U70-3] |
Protocols and materials databases
Antibodypediai | 17969, 264 antibodies |
DNASUi | 8861 |
Genome annotation databases
Ensembli | ENST00000361198; ENSP00000354616; ENSG00000198728 [Q86U70-2] ENST00000673968; ENSP00000501277; ENSG00000198728 [Q86U70-1] |
GeneIDi | 8861 |
KEGGi | hsa:8861 |
UCSCi | uc001kuk.6, human [Q86U70-1] |
Organism-specific databases
CTDi | 8861 |
DisGeNETi | 8861 |
EuPathDBi | HostDB:ENSG00000198728.10 |
GeneCardsi | LDB1 |
HGNCi | HGNC:6532, LDB1 |
HPAi | ENSG00000198728, Low tissue specificity |
MIMi | 603451, gene |
neXtProti | NX_Q86U70 |
OpenTargetsi | ENSG00000198728 |
PharmGKBi | PA30316 |
GenAtlasi | Search... |
Phylogenomic databases
eggNOGi | KOG2181, Eukaryota |
GeneTreei | ENSGT00390000005639 |
HOGENOMi | CLU_032597_0_0_1 |
InParanoidi | Q86U70 |
OMAi | KMSVGCA |
OrthoDBi | 849287at2759 |
PhylomeDBi | Q86U70 |
TreeFami | TF319923 |
Enzyme and pathway databases
PathwayCommonsi | Q86U70 |
Reactomei | R-HSA-8939236, RUNX1 regulates transcription of genes involved in differentiation of HSCs R-HSA-9010553, Regulation of expression of SLITs and ROBOs |
SIGNORi | Q86U70 |
Miscellaneous databases
BioGRID-ORCSi | 8861, 85 hits in 862 CRISPR screens |
ChiTaRSi | LDB1, human |
EvolutionaryTracei | Q86U70 |
GeneWikii | LDB1 |
GenomeRNAii | 8861 |
Pharosi | Q86U70, Tbio |
PROi | PR:Q86U70 |
RNActi | Q86U70, protein |
SOURCEi | Search... |
Gene expression databases
Bgeei | ENSG00000198728, Expressed in right ovary and 201 other tissues |
Genevisiblei | Q86U70, HS |
Family and domain databases
IDEALi | IID00282 |
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 |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | LDB1_HUMAN | |
Accessioni | Q86U70Primary (citable) accession number: Q86U70 Secondary accession number(s): B4DUC4 Q9UGM4 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | July 5, 2005 |
Last sequence update: | September 11, 2007 | |
Last modified: | December 2, 2020 | |
This is version 164 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program | |
Disclaimer | Any 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, Reference proteomeDocuments
- Human polymorphisms and disease mutations
Index of human polymorphisms and disease mutations - MIM cross-references
Online Mendelian Inheritance in Man (MIM) 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 - Human chromosome 10
Human chromosome 10: entries, gene names and cross-references to MIM - Human entries with polymorphisms or disease mutations
List of human entries with polymorphisms or disease mutations