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Protein

LIM domain-binding protein 1

Gene

LDB1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

GO - Molecular functioni

  • chromatin binding Source: Ensembl
  • enhancer sequence-specific DNA binding Source: Ensembl
  • 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 corepressor activity Source: ProtInc

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Enzyme and pathway databases

BioCyciZFISH:G66-32116-MONOMER.
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

HGNCiHGNC:6532. LDB1.

Subcellular locationi

GO - Cellular componenti

  • cell leading edge Source: UniProtKB
  • nuclear chromatin Source: BHF-UCL
  • nucleus Source: UniProtKB
  • protein complex Source: UniProtKB
  • transcription factor complex Source: BHF-UCL
Complete GO annotation...

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.

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.
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

WithEntry#Exp.IntActNotes
LHX6Q9UPM63EBI-677177,EBI-10258746
LHX8Q68G744EBI-11979761,EBI-8474075
LMO1P258005EBI-677177,EBI-8639312
LMO2P257916EBI-677177,EBI-739696
LMO2P25791-34EBI-11979761,EBI-11959475
LMO3Q8TAP4-44EBI-11979761,EBI-11742507
LMO4P619686EBI-677177,EBI-2798728
LMX1BO60663-23EBI-677177,EBI-10258690
SSBP3Q9BWW43EBI-677177,EBI-2902395

GO - Molecular functioni

  • 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

BioGridi114384. 38 interactors.
DIPiDIP-31826N.
IntActiQ86U70. 30 interactors.
MINTiMINT-233462.
STRINGi9606.ENSP00000392466.

Structurei

Secondary structure

1411
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi337 – 339Combined sources3
Turni346 – 349Combined sources4
Beta strandi355 – 357Combined sources3
Beta strandi359 – 362Combined sources4

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...

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

InterProiIPR030167. LDB1.
IPR029005. LIM-bd/SEUSS.
[Graphical view]
PANTHERiPTHR10378. PTHR10378. 1 hit.
PTHR10378:SF7. PTHR10378:SF7. 1 hit.

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 Publication1

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

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. 38 interactors.
DIPiDIP-31826N.
IntActiQ86U70. 30 interactors.
MINTiMINT-233462.
STRINGi9606.ENSP00000392466.

PTM databases

iPTMnetiQ86U70.
PhosphoSitePlusiQ86U70.

Polymorphism and mutation databases

BioMutaiLDB1.
DMDMi158518615.

Proteomic databases

EPDiQ86U70.
MaxQBiQ86U70.
PaxDbiQ86U70.
PeptideAtlasiQ86U70.
PRIDEiQ86U70.

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.
GeneCardsiLDB1.
H-InvDBHIX0009148.
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

BioCyciZFISH:G66-32116-MONOMER.
SIGNORiQ86U70.

Miscellaneous databases

ChiTaRSiLDB1. human.
EvolutionaryTraceiQ86U70.
GeneWikiiLDB1.
GenomeRNAii8861.
PROiQ86U70.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000198728.
CleanExiHS_LDB1.
GenevisibleiQ86U70. HS.

Family and domain databases

InterProiIPR030167. LDB1.
IPR029005. LIM-bd/SEUSS.
[Graphical view]
PANTHERiPTHR10378. PTHR10378. 1 hit.
PTHR10378:SF7. PTHR10378:SF7. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiLDB1_HUMAN
AccessioniPrimary (citable) accession number: Q86U70
Secondary accession number(s): B4DUC4
, O75479, O96010, Q1EQX1, Q9UGM4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 5, 2005
Last sequence update: September 11, 2007
Last modified: November 30, 2016
This is version 131 of the entry and version 2 of the sequence. [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

Miscellaneous

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

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 10
    Human chromosome 10: entries, gene names and cross-references to MIM
  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. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.