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Q86U70 (LDB1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 99. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:LDB1
Synonyms:CLIM2
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length411 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. May play a role in the development of motor neurons. 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.

Subunit structure

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 By similarity. Interacts with ESR1. Ref.10

Subcellular location

Nucleus Probable.

Tissue specificity

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. Ref.4

Domain

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

Post-translational modification

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

Miscellaneous

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

Sequence similarities

Belongs to the LDB family.

Sequence caution

The sequence CAB45409.1 differs from that shown. Reason: Erroneous initiation.

The sequence CAH72217.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
Polymorphism
   Molecular functionDevelopmental protein
   PTMUbl conjugation
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processWnt receptor signaling pathway

Inferred from electronic annotation. Source: Compara

anterior/posterior axis specification

Inferred from electronic annotation. Source: Compara

cellular component assembly

Inferred from electronic annotation. Source: Compara

cerebellar Purkinje cell differentiation

Inferred from electronic annotation. Source: Compara

epithelial structure maintenance

Inferred from electronic annotation. Source: Compara

gastrulation with mouth forming second

Inferred from electronic annotation. Source: Compara

hair follicle development

Inferred from electronic annotation. Source: Compara

head development

Inferred from electronic annotation. Source: Compara

histone H3-K4 acetylation

Inferred from sequence or structural similarity. Source: BHF-UCL

negative regulation of erythrocyte differentiation

Inferred from sequence or structural similarity. Source: UniProtKB

negative regulation of transcription, DNA-dependent

Inferred from direct assay PubMed 10767331. Source: UniProtKB

neuron differentiation

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of cell adhesion

Inferred from electronic annotation. Source: Compara

positive regulation of hemoglobin biosynthetic process

Inferred from sequence or structural similarity. Source: BHF-UCL

positive regulation of transcription from RNA polymerase II promoter

Inferred from mutant phenotype PubMed 20855495. Source: BHF-UCL

regulation of DNA-dependent transcription, elongation

Inferred from sequence or structural similarity. Source: BHF-UCL

somatic stem cell maintenance

Inferred from electronic annotation. Source: Compara

transcription from RNA polymerase II promoter

Inferred from electronic annotation. Source: Compara

transcription, DNA-dependent

Non-traceable author statement PubMed 12792813. Source: UniProtKB

transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery

Inferred from sequence or structural similarity. Source: BHF-UCL

   Cellular_componentcell-cell junction

Inferred from electronic annotation. Source: Compara

nuclear chromatin

Inferred from direct assay PubMed 20855495. Source: BHF-UCL

transcription factor complex

Inferred from direct assay PubMed 16314316. Source: BHF-UCL

   Molecular_functionLIM domain binding

Inferred from sequence or structural similarity. Source: UniProtKB

chromatin binding

Inferred from electronic annotation. Source: Compara

enhancer sequence-specific DNA binding

Inferred from electronic annotation. Source: Compara

protein homodimerization activity

Inferred from sequence or structural similarity. Source: UniProtKB

transcription corepressor activity

Traceable author statement PubMed 9391090. Source: ProtInc

Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q86U70-1)

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.
Note: No experimental confirmation available.
Isoform 2 (identifier: Q86U70-3)

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.
Isoform 3 (identifier: Q86U70-2)

Also known as: a;

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 411411LIM domain-binding protein 1
PRO_0000084384

Regions

Region336 – 37439LIM-binding domain (LID) By similarity

Natural variations

Alternative sequence1 – 3636Missing in isoform 2 and isoform 3.
VSP_027830
Alternative sequence336 – 35217DVMVV…GEFGD → VSISAFFSLLGCPTTHP in isoform 2.
VSP_027831
Alternative sequence353 – 41159Missing in isoform 2.
VSP_027832
Natural variant2991R → Q in a colorectal cancer sample; somatic mutation. Ref.13
VAR_036366

Experimental info

Mutagenesis245 – 2495LCVIL → ACVAA: Abolishes interaction with ESR1. Ref.10

Secondary structure

......... 411
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified September 11, 2007. Version 2.
Checksum: 5BB5348A36044580

FASTA41146,533
        10         20         30         40         50         60 
MSVGCACPGC SSKSFKLYSP KEPPNGNAFP PFHPGTMLDR DVGPTPMYPP TYLEPGIGRH 

        70         80         90        100        110        120 
TPYGNQTDYR IFELNKRLQN WTEECDNLWW DAFTTEFFED DAMLTITFCL EDGPKRYTIG 

       130        140        150        160        170        180 
RTLIPRYFRS IFEGGATELY YVLKHPKEAF HSNFVSLDCD QGSMVTQHGK PMFTQVCVEG 

       190        200        210        220        230        240 
RLYLEFMFDD MMRIKTWHFS IRQHRELIPR SILAMHAQDP QMLDQLSKNI TRCGLSNSTL 

       250        260        270        280        290        300 
NYLRLCVILE PMQELMSRHK TYSLSPRDCL KTCLFQKWQR MVAPPAEPTR QQPSKRRKRK 

       310        320        330        340        350        360 
MSGGSTMSSG GGNTNNSNSK KKSPASTFAL SSQVPDVMVV GEPTLMGGEF GDEDERLITR 

       370        380        390        400        410 
LENTQFDAAN GIDDEDSFNN SPALGANSPW NSKPPSSQES KSENPTSQAS Q 

« Hide

Isoform 2 (b) [UniParc].

Checksum: B086EB4D28FC8E56
Show »

FASTA31636,428
Isoform 3 (a) [UniParc].

Checksum: 698AC67CB5BD2DE7
Show »

FASTA37542,809

References

« Hide 'large scale' references
[1]"Cloning and chromosomal localization of two novel human genes encoding LIM-domain binding factors CLIM1 and CLIM2/LDB1/NLI."
Semina E.V., Altherr M.R., Murray J.C.
Mamm. Genome 9:921-924(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3).
Tissue: Craniofacial.
[2]"Genomic structure, alternative transcripts and chromosome location of the human LIM domain binding protein gene LDB1."
Drechsler M., Schumacher V., Friedrich S., Wildhardt G., Giesler S., Schroth A., Bodem J., Royer-Pokora B.
Cytogenet. Cell Genet. 87:119-124(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]"Isolation and chromosomal assignment of human genes encoding cofactor of LIM homeodomain proteins, CLIM1 and CLIM2."
Ueki N., Seki N., Yano K., Ohira M., Saito T., Masuho Y., Muramatsu M.
J. Hum. Genet. 44:112-115(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3).
Tissue: Brain.
[4]"Spliced isoforms of LIM-domain-binding protein (CLIM/NLI/Ldb) lacking the LIM-interaction domain."
Tran Y.H., Xu Z., Kato A., Mistry A.C., Goya Y., Taira M., Brandt S.J., Hirose S.
J. Biochem. 140:105-119(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), ALTERNATIVE SPLICING, TISSUE SPECIFICITY.
Tissue: Fetal brain.
[5]"Cloning, characterization, and physical mapping of the human homologs of the mouse C-LIM gene."
Phillips J.C., Goldman D.A., Wiggs J.L.
Submitted (MAY-1998) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3).
Tissue: Fetal brain.
[6]"Cloning of human full-length CDSs in BD Creator(TM) system donor vector."
Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A.
Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
[7]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
[8]"The DNA sequence and comparative analysis of human chromosome 10."
Deloukas P., Earthrowl M.E., Grafham D.V., Rubenfield M., French L., Steward C.A., Sims S.K., Jones M.C., Searle S., Scott C., Howe K., Hunt S.E., Andrews T.D., Gilbert J.G.R., Swarbreck D., Ashurst J.L., Taylor A., Battles J. expand/collapse author list , Bird C.P., Ainscough R., Almeida J.P., Ashwell R.I.S., Ambrose K.D., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Bates K., Beasley H., Bray-Allen S., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Cahill P., Camire D., Carter N.P., Chapman J.C., Clark S.Y., Clarke G., Clee C.M., Clegg S., Corby N., Coulson A., Dhami P., Dutta I., Dunn M., Faulkner L., Frankish A., Frankland J.A., Garner P., Garnett J., Gribble S., Griffiths C., Grocock R., Gustafson E., Hammond S., Harley J.L., Hart E., Heath P.D., Ho T.P., Hopkins B., Horne J., Howden P.J., Huckle E., Hynds C., Johnson C., Johnson D., Kana A., Kay M., Kimberley A.M., Kershaw J.K., Kokkinaki M., Laird G.K., Lawlor S., Lee H.M., Leongamornlert D.A., Laird G., Lloyd C., Lloyd D.M., Loveland J., Lovell J., McLaren S., McLay K.E., McMurray A., Mashreghi-Mohammadi M., Matthews L., Milne S., Nickerson T., Nguyen M., Overton-Larty E., Palmer S.A., Pearce A.V., Peck A.I., Pelan S., Phillimore B., Porter K., Rice C.M., Rogosin A., Ross M.T., Sarafidou T., Sehra H.K., Shownkeen R., Skuce C.D., Smith M., Standring L., Sycamore N., Tester J., Thorpe A., Torcasso W., Tracey A., Tromans A., Tsolas J., Wall M., Walsh J., Wang H., Weinstock K., West A.P., Willey D.L., Whitehead S.L., Wilming L., Wray P.W., Young L., Chen Y., Lovering R.C., Moschonas N.K., Siebert R., Fechtel K., Bentley D., Durbin R.M., Hubbard T., Doucette-Stamm L., Beck S., Smith D.R., Rogers J.
Nature 429:375-381(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[9]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
Tissue: Muscle.
[10]"Regulation of estrogen-dependent transcription by the LIM cofactors CLIM and RLIM in breast cancer."
Johnsen S.A., Guengoer C., Prenzel T., Riethdorf S., Riethdorf L., Taniguchi-Ishigaki N., Rau T., Tursun B., Furlow J.D., Sauter G., Scheffner M., Pantel K., Gannon F., Bach I.
Cancer Res. 69:128-136(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH ESR1, MUTAGENESIS OF 245-LEU--LEU-249, MISCELLANEOUS.
[11]"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Leukemic T-cell.
[12]"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[13]"The consensus coding sequences of human breast and colorectal cancers."
Sjoeblom T., Jones S., Wood L.D., Parsons D.W., Lin J., Barber T.D., Mandelker D., Leary R.J., Ptak J., Silliman N., Szabo S., Buckhaults P., Farrell C., Meeh P., Markowitz S.D., Willis J., Dawson D., Willson J.K.V. expand/collapse author list , Gazdar A.F., Hartigan J., Wu L., Liu C., Parmigiani G., Park B.H., Bachman K.E., Papadopoulos N., Vogelstein B., Kinzler K.W., Velculescu V.E.
Science 314:268-274(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANT [LARGE SCALE ANALYSIS] GLN-299.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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. Translation: CAH72217.1. Different initiation.
BC000482 mRNA. Translation: AAH00482.1.
BC009246 mRNA. Translation: AAH09246.1.
IPIIPI00428954.
IPI00760574.
IPI00856078.
RefSeqNP_001106878.1. NM_001113407.1.
NP_003884.1. NM_003893.4.
UniGeneHs.454418.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2XJYX-ray2.40B334-368[»]
2XJZX-ray2.80I/J/K/L/M334-368[»]
ProteinModelPortalQ86U70.
ModBaseSearch...

Protein-protein interaction databases

DIPDIP-31826N.
IntActQ86U70. 16 interactions.
MINTMINT-233462.
STRING9606.ENSP00000392466.

PTM databases

PhosphoSiteQ86U70.

Polymorphism databases

DMDM158518615.

Proteomic databases

PaxDbQ86U70.
PRIDEQ86U70.

Protocols and materials databases

DNASU8861.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000361198; ENSP00000354616; ENSG00000198728.
ENST00000425280; ENSP00000392466; ENSG00000198728.
GeneID8861.
KEGGhsa:8861.
UCSCuc001kuk.4. human.
uc001kul.3. human.

Organism-specific databases

CTD8861.
GeneCardsGC10M103857.
H-InvDBHIX0009148.
HGNCHGNC:6532. LDB1.
HPAHPA034488.
MIM603451. gene.
neXtProtNX_Q86U70.
PharmGKBPA30316.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG282114.
HOGENOMHOG000030908.
HOVERGENHBG000135.
InParanoidQ86U70.
KOK15617.
OMAGSNSPWN.
OrthoDBEOG4XWFXV.

Gene expression databases

BgeeQ86U70.
CleanExHS_LDB1.
GenevestigatorQ86U70.
GermOnlineENSG00000198728. Homo sapiens.

Family and domain databases

InterProIPR002691. LIM-dom-bd.
[Graphical view]
PANTHERPTHR10378. PTHR10378. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceQ86U70.
GenomeRNAi8861.
NextBio33273.
SOURCESearch...

Entry information

Entry nameLDB1_HUMAN
AccessionPrimary (citable) accession number: Q86U70
Secondary accession number(s): B4DUC4 expand/collapse secondary AC list , O75479, O96010, Q1EQX1, Q9UGM4
Entry history
Integrated into UniProtKB/Swiss-Prot: July 5, 2005
Last sequence update: September 11, 2007
Last modified: May 1, 2013
This is version 99 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

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

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