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Protein

Lymphotoxin-beta

Gene

LTB

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Cytokine that binds to LTBR/TNFRSF3. May play a specific role in immune response regulation. Provides the membrane anchor for the attachment of the heterotrimeric complex to the cell surface. Isoform 2 is probably non-functional.

GO - Molecular functioni

  • cytokine activity Source: UniProtKB-KW
  • receptor binding Source: ProtInc
  • tumor necrosis factor receptor binding Source: InterPro

GO - Biological processi

Keywordsi

Molecular functionCytokine

Enzyme and pathway databases

ReactomeiR-HSA-5668541. TNFR2 non-canonical NF-kB pathway.
R-HSA-5676594. TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway.
SIGNORiQ06643.

Names & Taxonomyi

Protein namesi
Recommended name:
Lymphotoxin-beta
Short name:
LT-beta
Alternative name(s):
Tumor necrosis factor C
Short name:
TNF-C
Tumor necrosis factor ligand superfamily member 3
Gene namesi
Name:LTB
Synonyms:TNFC, TNFSF3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

EuPathDBiHostDB:ENSG00000227507.2.
HGNCiHGNC:6711. LTB.

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

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 18CytoplasmicSequence analysisAdd BLAST18
Transmembranei19 – 48Helical; Signal-anchor for type II membrane proteinSequence analysisAdd BLAST30
Topological domaini49 – 244ExtracellularSequence analysisAdd BLAST196

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Organism-specific databases

DisGeNETi4050.
OpenTargetsiENSG00000227507.
PharmGKBiPA30475.

Chemistry databases

ChEMBLiCHEMBL3833421.

Polymorphism and mutation databases

BioMutaiLTB.
DMDMi549088.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001854861 – 244Lymphotoxin-betaAdd BLAST244

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi222N-linked (GlcNAc...) asparagineSequence analysis1

Keywords - PTMi

Glycoprotein

Proteomic databases

PaxDbiQ06643.
PeptideAtlasiQ06643.
PRIDEiQ06643.

PTM databases

PhosphoSitePlusiQ06643.

Expressioni

Tissue specificityi

Spleen and thymus.

Gene expression databases

BgeeiENSG00000227507.
CleanExiHS_LTB.
ExpressionAtlasiQ06643. baseline and differential.
GenevisibleiQ06643. HS.

Organism-specific databases

HPAiHPA048884.

Interactioni

Subunit structurei

Heterotrimer of either two LTB and one LTA subunits or (less prevalent) one LTB and two LTA subunits.

GO - Molecular functioni

  • cytokine activity Source: UniProtKB-KW
  • receptor binding Source: ProtInc
  • tumor necrosis factor receptor binding Source: InterPro

Protein-protein interaction databases

BioGridi110228. 2 interactors.
CORUMiQ06643.
DIPiDIP-2996N.
IntActiQ06643. 5 interactors.
STRINGi9606.ENSP00000410481.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4MXWX-ray3.60B/D/Y/Z86-244[»]
ProteinModelPortaliQ06643.
SMRiQ06643.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the tumor necrosis factor family.Curated

Keywords - Domaini

Signal-anchor, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410IJP9. Eukaryota.
ENOG410ZHBF. LUCA.
GeneTreeiENSGT00390000007066.
HOGENOMiHOG000273916.
HOVERGENiHBG000209.
InParanoidiQ06643.
KOiK03157.
OMAiYCHVGYR.
OrthoDBiEOG091G0J9M.
PhylomeDBiQ06643.
TreeFamiTF337780.

Family and domain databases

Gene3Di2.60.120.40. 1 hit.
InterProiView protein in InterPro
IPR006053. TNF.
IPR002961. TNF_C.
IPR021184. TNF_CS.
IPR006052. TNF_dom.
IPR008983. Tumour_necrosis_fac-like_dom.
PANTHERiPTHR11471:SF29. PTHR11471:SF29. 1 hit.
PfamiView protein in Pfam
PF00229. TNF. 1 hit.
PRINTSiPR01234. TNECROSISFCT.
PR01237. TNFC.
SMARTiView protein in SMART
SM00207. TNF. 1 hit.
SUPFAMiSSF49842. SSF49842. 1 hit.
PROSITEiView protein in PROSITE
PS00251. TNF_1. 1 hit.
PS50049. TNF_2. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q06643-1) [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
MGALGLEGRG GRLQGRGSLL LAVAGATSLV TLLLAVPITV LAVLALVPQD
60 70 80 90 100
QGGLVTETAD PGAQAQQGLG FQKLPEEEPE TDLSPGLPAA HLIGAPLKGQ
110 120 130 140 150
GLGWETTKEQ AFLTSGTQFS DAEGLALPQD GLYYLYCLVG YRGRAPPGGG
160 170 180 190 200
DPQGRSVTLR SSLYRAGGAY GPGTPELLLE GAETVTPVLD PARRQGYGPL
210 220 230 240
WYTSVGFGGL VQLRRGERVY VNISHPDMVD FARGKTFFGA VMVG
Length:244
Mass (Da):25,390
Last modified:June 1, 1994 - v1
Checksum:iF41569459830ED4C
GO
Isoform 2 (identifier: Q06643-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     53-77: GLVTETADPGAQAQQGLGFQKLPEE → GLGFRSCQRRSQKQISAPGSQLPTS
     78-244: Missing.

Show »
Length:77
Mass (Da):7,780
Checksum:i8F1256D793D85397
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti60 – 69DPGAQAQQGL → GLSAPGSGRT in AAB37342 (PubMed:9299492).Curated10

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_01302570G → E1 PublicationCorresponds to variant dbSNP:rs3093554Ensembl.1
Natural variantiVAR_01633184S → R1 PublicationCorresponds to variant dbSNP:rs4647186Ensembl.1
Natural variantiVAR_01633287L → F1 PublicationCorresponds to variant dbSNP:rs4647187Ensembl.1
Natural variantiVAR_013026111A → P1 PublicationCorresponds to variant dbSNP:rs3093555Ensembl.1
Natural variantiVAR_029145122A → D. Corresponds to variant dbSNP:rs2229699Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_00644153 – 77GLVTE…KLPEE → GLGFRSCQRRSQKQISAPGS QLPTS in isoform 2. 3 PublicationsAdd BLAST25
Alternative sequenceiVSP_00644278 – 244Missing in isoform 2. 3 PublicationsAdd BLAST167

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L11016 Genomic DNA. Translation: AAA99888.1.
U89922 mRNA. Translation: AAC51769.1.
U79029 mRNA. Translation: AAB37342.1.
L11015 mRNA. Translation: AAA36191.1.
Y14768 Genomic DNA. Translation: CAA75069.1.
AF129756 Genomic DNA. Translation: AAD18089.1.
BA000025 Genomic DNA. Translation: BAB63395.1.
AY070219 Genomic DNA. Translation: AAL49954.1.
AY070219 Genomic DNA. Translation: AAL49955.1.
AY216497 Genomic DNA. Translation: AAO21134.1.
AK312210 mRNA. Translation: BAG35143.1.
CH471081 Genomic DNA. Translation: EAX03425.1.
BC069330 mRNA. Translation: AAH69330.1.
BC093783 mRNA. Translation: AAH93783.1.
CCDSiCCDS4703.1. [Q06643-1]
CCDS4704.1. [Q06643-2]
PIRiA46066.
JC5645.
RefSeqiNP_002332.1. NM_002341.1. [Q06643-1]
NP_033666.1. NM_009588.1. [Q06643-2]
UniGeneiHs.376208.

Genome annotation databases

EnsembliENST00000376117; ENSP00000365285; ENSG00000204487. [Q06643-1]
ENST00000383493; ENSP00000372985; ENSG00000206437. [Q06643-1]
ENST00000420402; ENSP00000398741; ENSG00000223448. [Q06643-1]
ENST00000421268; ENSP00000393693; ENSG00000238114. [Q06643-1]
ENST00000429299; ENSP00000410481; ENSG00000227507. [Q06643-1]
ENST00000444479; ENSP00000395102; ENSG00000236925. [Q06643-1]
ENST00000446745; ENSP00000416113; ENSG00000227507. [Q06643-2]
ENST00000456113; ENSP00000404014; ENSG00000236237. [Q06643-1]
ENST00000457552; ENSP00000404450; ENSG00000231314. [Q06643-1]
GeneIDi4050.
KEGGihsa:4050.
UCSCiuc003nul.4. human. [Q06643-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Entry informationi

Entry nameiTNFC_HUMAN
AccessioniPrimary (citable) accession number: Q06643
Secondary accession number(s): P78370, Q52LU8, Q99761
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: June 1, 1994
Last modified: November 22, 2017
This is version 163 of the entry and version 1 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, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 6
    Human chromosome 6: 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