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Protein

LIM domain-binding protein 3

Gene

Ldb3

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

May function as an adapter in striated muscle to couple protein kinase C-mediated signaling via its LIM domains to the cytoskeleton.1 Publication

GO - Molecular functioni

  • cytoskeletal protein binding Source: MGI
  • metal ion binding Source: UniProtKB-KW
  • muscle alpha-actinin binding Source: MGI
  • protein kinase C binding Source: UniProtKB

GO - Biological processi

  • sarcomere organization Source: MGI

Keywordsi

LigandMetal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
LIM domain-binding protein 3
Alternative name(s):
Protein cypher
Protein oracle
Z-band alternatively spliced PDZ-motif protein
Gene namesi
Name:Ldb3Imported
Synonyms:Kiaa0613
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 14

Organism-specific databases

MGIiMGI:1344412. Ldb3.

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

Cell projection, Cytoplasm, Cytoskeleton

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000757681 – 723LIM domain-binding protein 3Add BLAST723

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei44PhosphoserineCombined sources1
Modified residuei98PhosphoserineCombined sources1
Modified residuei119PhosphothreonineCombined sources1
Modified residuei121PhosphoserineCombined sources1
Modified residuei123PhosphoserineCombined sources1
Modified residuei214PhosphoserineCombined sources1
Modified residuei216Omega-N-methylarginineCombined sources1
Modified residuei220PhosphoserineCombined sources1
Modified residuei251PhosphoserineCombined sources1
Modified residuei512Omega-N-methylarginineCombined sources1
Modified residuei529Omega-N-methylarginineCombined sources1
Isoform 21 Publication (identifier: Q9JKS4-2)
Modified residuei112PhosphoserineCombined sourcesCurated1
Isoform 41 Publication (identifier: Q9JKS4-4)
Modified residuei112PhosphoserineCombined sources1
Modified residuei291Omega-N-methylarginineCombined sources1
Isoform 62 Publications (identifier: Q9JKS4-6)
Modified residuei112PhosphoserineCombined sources1
Modified residuei288PhosphoserineCombined sources1
Isoform 51 Publication (identifier: Q9JKS4-5)
Modified residuei327PhosphoserineCombined sources1
Isoform 32 Publications (identifier: Q9JKS4-3)
Modified residuei330Omega-N-methylarginineCombined sources1

Keywords - PTMi

Methylation, Phosphoprotein

Proteomic databases

PaxDbiQ9JKS4.
PeptideAtlasiQ9JKS4.
PRIDEiQ9JKS4.

PTM databases

iPTMnetiQ9JKS4.
PhosphoSitePlusiQ9JKS4.

Expressioni

Tissue specificityi

Expressed primarily in adult heart and skeletal muscle, and detected at lower levels in lung. Isoforms are expressed in a tissue-specific manner. Isoform 1, isoform 3 and isoform 5 are expressed in heart, whereas isoform 2, isoform 4 and isoform 6 are expressed in skeletal muscle.4 Publications

Developmental stagei

Initially expressed in a myocardium-specific manner at 8.5-9 dpc and remains cardiac-restricted until day 12. Strongly expressed throughout heart in all stages examined. At 12.5 dpc expressed at low levels in non-cardiac striated muscles. By day E14.5 expressed at high levels in both cardiac and skeletal muscle, and also strongly expressed in striated muscles of tongue, thoracic and abdominal muscles, leg and diaphragm. The various isoforms are developmentally regulated in both skeletal and cardiac muscle. Isoform 5 and isoform 6, which are barely detectable during embryogenesis are up-regulated postnatally. In heart, isoform 3 is up-regulated developmentally, whereas the predominant isoform 1 is expressed throughout development and into adulthood. In skeletal muscle, the predominant isoform 2 is gradually replaced by isoform 4 postnatally.2 Publications

Gene expression databases

BgeeiENSMUSG00000021798.
CleanExiMM_LDB3.
ExpressionAtlasiQ9JKS4. baseline and differential.
GenevisibleiQ9JKS4. MM.

Interactioni

Subunit structurei

Interacts via its LIM domains with various PKC isoforms. Interacts via its PDZ domain with the ACTN2 C-terminal region. Interacts with MYOZ1, MYOZ2 and MYOZ3.By similarity1 Publication

Binary interactionsi

Show more details

GO - Molecular functioni

  • cytoskeletal protein binding Source: MGI
  • muscle alpha-actinin binding Source: MGI
  • protein kinase C binding Source: UniProtKB

Protein-protein interaction databases

BioGridi204912. 9 interactors.
IntActiQ9JKS4. 8 interactors.
MINTiMINT-97840.
STRINGi10090.ENSMUSP00000022327.

Structurei

Secondary structure

1723
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 10Combined sources9
Beta strandi15 – 17Combined sources3
Turni21 – 24Combined sources4
Beta strandi28 – 32Combined sources5
Helixi37 – 40Combined sources4
Beta strandi48 – 54Combined sources7
Beta strandi56 – 60Combined sources5
Helixi62 – 71Combined sources10
Beta strandi74 – 81Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1WJLNMR-A1-83[»]
ProteinModelPortaliQ9JKS4.
SMRiQ9JKS4.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9JKS4.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 84PDZPROSITE-ProRule annotationAdd BLAST84
Domaini545 – 603LIM zinc-binding 1PROSITE-ProRule annotationAdd BLAST59
Domaini604 – 663LIM zinc-binding 2PROSITE-ProRule annotationAdd BLAST60
Domaini664 – 723LIM zinc-binding 3PROSITE-ProRule annotationAdd BLAST60

Keywords - Domaini

LIM domain, Repeat

Phylogenomic databases

eggNOGiKOG1703. Eukaryota.
ENOG410XRD4. LUCA.
GeneTreeiENSGT00760000118910.
HOVERGENiHBG051478.
InParanoidiQ9JKS4.
KOiK19867.
OMAiCTSQATT.
OrthoDBiEOG091G0A45.
PhylomeDBiQ9JKS4.
TreeFamiTF106408.

Family and domain databases

InterProiView protein in InterPro
IPR031847. DUF4749.
IPR001478. PDZ.
IPR006643. Zasp-like_motif.
IPR001781. Znf_LIM.
PfamiView protein in Pfam
PF15936. DUF4749. 1 hit.
PF00412. LIM. 3 hits.
PF00595. PDZ. 1 hit.
SMARTiView protein in SMART
SM00132. LIM. 3 hits.
SM00228. PDZ. 1 hit.
SM00735. ZM. 1 hit.
SUPFAMiSSF50156. SSF50156. 1 hit.
PROSITEiView protein in PROSITE
PS00478. LIM_DOMAIN_1. 2 hits.
PS50023. LIM_DOMAIN_2. 3 hits.
PS50106. PDZ. 1 hit.

Sequences (6)i

Sequence statusi: Complete.

This entry describes 6 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 11 Publication (identifier: Q9JKS4-1) [UniParc]FASTAAdd to basket
Also known as: Cypher1c1 Publication, Oracle 11 Publication

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
MSYSVTLTGP GPWGFRLQGG KDFNMPLTIS RITPGSKAAQ SQLSQGDLVV
60 70 80 90 100
AIDGVNTDTM THLEAQNKIK SASYNLSLTL QKSKRPIPIS TTAPPIQSPL
110 120 130 140 150
PVIPHQKDPA LDTNGSLATP SPSPEARASP GALEFGDTFS SSFSQTSVCS
160 170 180 190 200
PLMEASGPVL PLGSPVAKAS SEGAQGSVSP KVLPGPSQPR QYNNPIGLYS
210 220 230 240 250
AETLREMAQM YQMSLRGKAS GAGLLGGSLP VKDLAVDSAS PVYQAVIKTQ
260 270 280 290 300
SKPEDEADEW ARRSSNLQSR SFRILAQMTG TEYMQDPDEE ALRRSSTPIE
310 320 330 340 350
HAPVCTSQAT SPLLPASAQS PAAASPIAAS PTLATAAATH AAAASAAGPA
360 370 380 390 400
ASPVENPRPQ ASAYSPAAAA SPAPSAHTSY SEGPAAPAPK PRVVTTASIR
410 420 430 440 450
PSVYQPVPAS SYSPSPGANY SPTPYTPSPA PAYTPSPAPT YTPSPAPTYS
460 470 480 490 500
PSPAPAYTPS PAPNYTPTPS AAYSGGPSES ASRPPWVTDD SFSQKFAPGK
510 520 530 540 550
STTTVSKQTL PRGAPAYNPT GPQVTPLARG TFQRAERFPA SSRTPLCGHC
560 570 580 590 600
NNVIRGPFLV AMGRSWHPEE FNCAYCKTSL ADVCFVEEQN NVYCERCYEQ
610 620 630 640 650
FFAPICAKCN TKIMGEVMHA LRQTWHTTCF VCAACKKPFG NSLFHMEDGE
660 670 680 690 700
PYCEKDYINL FSTKCHGCDF PVEAGDKFIE ALGHTWHDTC FICAVCHVNL
710 720
EGQPFYSKKD KPLCKKHAHA INV
Length:723
Mass (Da):76,432
Last modified:October 1, 2000 - v1
Checksum:iCC67D38AC2FFA6B6
GO
Isoform 21 Publication (identifier: Q9JKS4-2) [UniParc]FASTAAdd to basket
Also known as: Cypher1s1 Publication

The sequence of this isoform differs from the canonical sequence as follows:
     108-227: DPALDTNGSL...KASGAGLLGG → VVANSPANAD...SDFSGASPLA

Show »
Length:684
Mass (Da):72,752
Checksum:iB8969D96ECC7C7C5
GO
Isoform 32 Publications (identifier: Q9JKS4-3) [UniParc]FASTAAdd to basket
Also known as: Cypher3c1 Publication, Oracle 21 Publication

The sequence of this isoform differs from the canonical sequence as follows:
     296-357: Missing.

Show »
Length:661
Mass (Da):70,751
Checksum:i5DEFEEE78D45532F
GO
Isoform 41 Publication (identifier: Q9JKS4-4) [UniParc]FASTAAdd to basket
Also known as: Cypher3s1 Publication

The sequence of this isoform differs from the canonical sequence as follows:
     108-227: DPALDTNGSL...KASGAGLLGG → VVANSPANAD...SDFSGASPLA
     296-357: Missing.

Show »
Length:622
Mass (Da):67,071
Checksum:iABC92BB80C3B9903
GO
Isoform 51 Publication (identifier: Q9JKS4-5) [UniParc]FASTAAdd to basket
Also known as: Cypher2c1 Publication

The sequence of this isoform differs from the canonical sequence as follows:
     296-327: STPIEHAPVCTSQATSPLLPASAQSPAAASPI → RERFETERNSPRFAKLRNWHHGLSAQILNVKS
     328-723: Missing.

Show »
Length:327
Mass (Da):35,108
Checksum:i603BEF5D6152B848
GO
Isoform 62 Publications (identifier: Q9JKS4-6) [UniParc]FASTAAdd to basket
Also known as: Cypher2s1 Publication

The sequence of this isoform differs from the canonical sequence as follows:
     108-227: DPALDTNGSL...KASGAGLLGG → VVANSPANAD...SDFSGASPLA
     296-327: STPIEHAPVCTSQATSPLLPASAQSPAAASPI → RERFETERNSPRFAKLRNWHHGLSAQILNVKS
     328-723: Missing.

Show »
Length:288
Mass (Da):31,427
Checksum:i65B11275409291B6
GO

Sequence cautioni

The sequence BAB23128 differs from that shown. Sequencing errors.Curated
The sequence BAD32258 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti108 – 145DPALD…SSFSQ → VVANSPANADYQERFNPSVL KGLSSVLKGLSSVHPQAH in BAB23128 (PubMed:16141072).CuratedAdd BLAST38
Sequence conflicti450S → T in AAD42950 (PubMed:10391924).Curated1
Sequence conflicti450S → T in AAO26188 (PubMed:12499364).Curated1
Sequence conflicti450S → T in AAO26189 (PubMed:12499364).Curated1
Sequence conflicti512R → W in BAD32258 (PubMed:15368895).Curated1
Isoform 21 Publication (identifier: Q9JKS4-2)
Sequence conflicti176 – 188AQGSD…ASPLA → AQGSDFSG in AAO26189 (PubMed:12499364).Combined sourcesCuratedAdd BLAST13

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_051903108 – 227DPALD…GLLGG → VVANSPANADYQERFNPSVL KDSALSTHKPIEVKGLGGKA TIIHAQYNTPISMYSQDAIM DAIAGQAQAQGSDFSGASPL A in isoform 2, isoform 4 and isoform 6. 5 PublicationsAdd BLAST120
Alternative sequenceiVSP_051904296 – 357Missing in isoform 3 and isoform 4. 3 PublicationsAdd BLAST62
Alternative sequenceiVSP_051905296 – 327STPIE…AASPI → RERFETERNSPRFAKLRNWH HGLSAQILNVKS in isoform 5 and isoform 6. 5 PublicationsAdd BLAST32
Alternative sequenceiVSP_051906328 – 723Missing in isoform 5 and isoform 6. 5 PublicationsAdd BLAST396

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF114378 mRNA. Translation: AAD42950.2.
AF114379 mRNA. Translation: AAD42951.2.
AJ005621 mRNA. Translation: CAB46747.1.
AF228057 mRNA. Translation: AAF33847.1.
AF228058 mRNA. Translation: AAF33848.1.
AY206011 mRNA. Translation: AAO26187.1.
AY206012 mRNA. Translation: AAO26188.1.
AY206013 mRNA. Translation: AAO26189.1.
AY206015 mRNA. Translation: AAO26190.1.
AK172980 mRNA. Translation: BAD32258.1. Different initiation.
AK004020 mRNA. Translation: BAB23128.1. Sequence problems.
AK137181 mRNA. Translation: BAE23262.1.
AK142292 mRNA. Translation: BAE25016.1.
BC099596 mRNA. Translation: AAH99596.1.
BC138793 mRNA. Translation: AAI38794.1.
BC145420 mRNA. Translation: AAI45421.1.
CCDSiCCDS26940.1. [Q9JKS4-3]
CCDS26941.1. [Q9JKS4-1]
CCDS26942.1. [Q9JKS4-5]
CCDS36879.1. [Q9JKS4-2]
RefSeqiNP_001034160.1. NM_001039071.2. [Q9JKS4-3]
NP_001034161.1. NM_001039072.2.
NP_001034162.1. NM_001039073.2. [Q9JKS4-4]
NP_001034163.1. NM_001039074.2. [Q9JKS4-2]
NP_001034164.1. NM_001039075.2. [Q9JKS4-6]
NP_001034165.1. NM_001039076.2. [Q9JKS4-5]
NP_036048.3. NM_011918.4. [Q9JKS4-1]
XP_006519080.1. XM_006519017.3. [Q9JKS4-2]
XP_017171508.1. XM_017316019.1. [Q9JKS4-1]
UniGeneiMm.29733.

Genome annotation databases

EnsembliENSMUST00000022327; ENSMUSP00000022327; ENSMUSG00000021798. [Q9JKS4-1]
ENSMUST00000022328; ENSMUSP00000022328; ENSMUSG00000021798. [Q9JKS4-3]
ENSMUST00000022330; ENSMUSP00000022330; ENSMUSG00000021798. [Q9JKS4-5]
ENSMUST00000090040; ENSMUSP00000087494; ENSMUSG00000021798. [Q9JKS4-2]
GeneIDi24131.
KEGGimmu:24131.
UCSCiuc007taz.1. mouse. [Q9JKS4-2]
uc007tba.1. mouse. [Q9JKS4-4]
uc007tbc.1. mouse. [Q9JKS4-1]
uc007tbd.1. mouse. [Q9JKS4-3]
uc007tbe.1. mouse. [Q9JKS4-6]
uc007tbf.1. mouse. [Q9JKS4-5]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiLDB3_MOUSE
AccessioniPrimary (citable) accession number: Q9JKS4
Secondary accession number(s): B2RSB0
, B7ZNT6, Q6A038, Q811P2, Q811P3, Q811P4, Q811P5, Q9D130, Q9JKS3, Q9R0Z1, Q9WVH1, Q9WVH2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 6, 2005
Last sequence update: October 1, 2000
Last modified: September 27, 2017
This is version 137 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references