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Protein

LIM domain-binding protein 1

Gene

LDB1

Organism
Homo sapiens (Human)
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 (By similarity).By similarity

Miscellaneous

Acts as a negative coregulator of ESR1-mediated transcription in breast cancer cells.

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDevelopmental protein

Enzyme and pathway databases

ReactomeiR-HSA-8939236 RUNX1 regulates transcription of genes involved in differentiation of HSCs
R-HSA-9010553 Regulation of expression of SLITs and ROBOs
SIGNORiQ86U70

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:
hLdb1
Nuclear LIM interactor
Gene namesi
Name:LDB1
Synonyms:CLIM2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 10

Organism-specific databases

EuPathDBiHostDB:ENSG00000198728.10
HGNCiHGNC:6532 LDB1
MIMi603451 gene
neXtProtiNX_Q86U70

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

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi245 – 249LCVIL → ACVAA: Abolishes interaction with ESR1. 1 Publication5

Organism-specific databases

DisGeNETi8861
OpenTargetsiENSG00000198728
PharmGKBiPA30316

Polymorphism and mutation databases

BioMutaiLDB1
DMDMi158518615

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00000843842 – 411LIM domain-binding protein 1Add BLAST410

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineCombined sources1
Modified residuei61PhosphothreonineBy similarity1
Modified residuei265PhosphoserineCombined sources1
Modified residuei302PhosphoserineBy similarity1

Post-translational modificationi

Ubiquitinated by RLIM/RNF12, leading to its degradation by the proteasome.By similarity

Keywords - PTMi

Acetylation, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ86U70
MaxQBiQ86U70
PaxDbiQ86U70
PeptideAtlasiQ86U70
PRIDEiQ86U70
ProteomicsDBi69771
69772 [Q86U70-2]
69773 [Q86U70-3]

PTM databases

iPTMnetiQ86U70
PhosphoSitePlusiQ86U70

Expressioni

Tissue specificityi

Expressed in a wide range of adult tissues including brain, heart, skeletal muscle, colon, thymus, spleen, kidney, liver, small intestine, lung and peripheral blood leukocytes.1 Publication

Gene expression databases

BgeeiENSG00000198728 Expressed in 188 organ(s), highest expression level in right ovary
CleanExiHS_LDB1
GenevisibleiQ86U70 HS

Organism-specific databases

HPAiHPA034488

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).By similarity2 Publications

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi114384, 41 interactors
CORUMiQ86U70
DIPiDIP-31826N
IntActiQ86U70, 34 interactors
MINTiQ86U70
STRINGi9606.ENSP00000392466

Structurei

Secondary structure

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

3D structure databases

ProteinModelPortaliQ86U70
SMRiQ86U70
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ86U70

Family & Domainsi

Region

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

Domaini

The dimerization domain is located in the N-terminus.By similarity

Sequence similaritiesi

Belongs to the LDB family.Curated

Phylogenomic databases

eggNOGiKOG2181 Eukaryota
ENOG410YZVH LUCA
GeneTreeiENSGT00390000005639
HOGENOMiHOG000030908
HOVERGENiHBG000135
InParanoidiQ86U70
KOiK15617
OMAiKMSVGCA
OrthoDBiEOG091G0A0P
PhylomeDBiQ86U70
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
Isoform 1 (identifier: Q86U70-1) [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
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
Note: No experimental confirmation available.
Length:411
Mass (Da):46,533
Last modified:September 11, 2007 - v2
Checksum:i5BB5348A36044580
GO
Isoform 2 (identifier: Q86U70-3) [UniParc]FASTAAdd to basket
Also known as: b

The sequence of this isoform differs from the canonical sequence as follows:
     1-36: Missing.
     336-352: DVMVVGEPTLMGGEFGD → VSISAFFSLLGCPTTHP
     353-411: Missing.

Note: Due to intron retention. Lacks LIM-binding domain.
Show »
Length:316
Mass (Da):36,428
Checksum:iB086EB4D28FC8E56
GO
Isoform 3 (identifier: Q86U70-2) [UniParc]FASTAAdd to basket
Also known as: a

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

Show »
Length:375
Mass (Da):42,809
Checksum:i698AC67CB5BD2DE7
GO

Sequence cautioni

The sequence CAB45409 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_036366299R → Q in a colorectal cancer sample; somatic mutation. 1 PublicationCorresponds to variant dbSNP:rs990101456Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0278301 – 36Missing in isoform 2 and isoform 3. 7 PublicationsAdd BLAST36
Alternative sequenceiVSP_027831336 – 352DVMVV…GEFGD → VSISAFFSLLGCPTTHP in isoform 2. 2 PublicationsAdd BLAST17
Alternative sequenceiVSP_027832353 – 411Missing in isoform 2. 2 PublicationsAdd BLAST59

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
CCDSiCCDS44472.1 [Q86U70-1]
CCDS7528.1 [Q86U70-2]
RefSeqiNP_001106878.1, NM_001113407.2 [Q86U70-1]
NP_003884.1, NM_003893.4 [Q86U70-2]
UniGeneiHs.454418
Hs.672935

Genome annotation databases

EnsembliENST00000361198; ENSP00000354616; ENSG00000198728 [Q86U70-2]
ENST00000425280; ENSP00000392466; ENSG00000198728 [Q86U70-1]
GeneIDi8861
KEGGihsa:8861
UCSCiuc001kuk.6 human [Q86U70-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar 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
CCDSiCCDS44472.1 [Q86U70-1]
CCDS7528.1 [Q86U70-2]
RefSeqiNP_001106878.1, NM_001113407.2 [Q86U70-1]
NP_003884.1, NM_003893.4 [Q86U70-2]
UniGeneiHs.454418
Hs.672935

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2XJYX-ray2.40B334-368[»]
2XJZX-ray2.80I/J/K/L/M334-368[»]
2YPAX-ray2.80D336-375[»]
ProteinModelPortaliQ86U70
SMRiQ86U70
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114384, 41 interactors
CORUMiQ86U70
DIPiDIP-31826N
IntActiQ86U70, 34 interactors
MINTiQ86U70
STRINGi9606.ENSP00000392466

PTM databases

iPTMnetiQ86U70
PhosphoSitePlusiQ86U70

Polymorphism and mutation databases

BioMutaiLDB1
DMDMi158518615

Proteomic databases

EPDiQ86U70
MaxQBiQ86U70
PaxDbiQ86U70
PeptideAtlasiQ86U70
PRIDEiQ86U70
ProteomicsDBi69771
69772 [Q86U70-2]
69773 [Q86U70-3]

Protocols and materials databases

DNASUi8861
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000361198; ENSP00000354616; ENSG00000198728 [Q86U70-2]
ENST00000425280; ENSP00000392466; ENSG00000198728 [Q86U70-1]
GeneIDi8861
KEGGihsa:8861
UCSCiuc001kuk.6 human [Q86U70-1]

Organism-specific databases

CTDi8861
DisGeNETi8861
EuPathDBiHostDB:ENSG00000198728.10
GeneCardsiLDB1
H-InvDBiHIX0009148
HGNCiHGNC:6532 LDB1
HPAiHPA034488
MIMi603451 gene
neXtProtiNX_Q86U70
OpenTargetsiENSG00000198728
PharmGKBiPA30316
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2181 Eukaryota
ENOG410YZVH LUCA
GeneTreeiENSGT00390000005639
HOGENOMiHOG000030908
HOVERGENiHBG000135
InParanoidiQ86U70
KOiK15617
OMAiKMSVGCA
OrthoDBiEOG091G0A0P
PhylomeDBiQ86U70
TreeFamiTF319923

Enzyme and pathway databases

ReactomeiR-HSA-8939236 RUNX1 regulates transcription of genes involved in differentiation of HSCs
R-HSA-9010553 Regulation of expression of SLITs and ROBOs
SIGNORiQ86U70

Miscellaneous databases

ChiTaRSiLDB1 human
EvolutionaryTraceiQ86U70
GeneWikiiLDB1
GenomeRNAii8861
PROiPR:Q86U70
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000198728 Expressed in 188 organ(s), highest expression level in right ovary
CleanExiHS_LDB1
GenevisibleiQ86U70 HS

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_HUMAN
AccessioniPrimary (citable) accession number: Q86U70
Secondary accession number(s): B4DUC4
, O75479, O96010, Q1EQX1, Q9UGM4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 5, 2005
Last sequence update: September 11, 2007
Last modified: November 7, 2018
This is version 148 of the entry and version 2 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, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. Human chromosome 10
    Human chromosome 10: entries, gene names and cross-references to MIM
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