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Protein

Lymphotoxin-beta

Gene

LTB

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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
  • signaling 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
MIMi600978 gene
neXtProtiNX_Q06643

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
ProteomicsDBi58468
58469 [Q06643-2]

PTM databases

PhosphoSitePlusiQ06643

Expressioni

Tissue specificityi

Spleen and thymus.

Gene expression databases

BgeeiENSG00000227507 Expressed in 161 organ(s), highest expression level in adrenal gland
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

Protein-protein interaction databases

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

Structurei

3D structure databases

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

CDDicd00184 TNF, 1 hit
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

Cross-referencesi

Web resourcesi

NIEHS-SNPs
SeattleSNPs

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

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...

Protein-protein interaction databases

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

Chemistry databases

ChEMBLiCHEMBL3833421

PTM databases

PhosphoSitePlusiQ06643

Polymorphism and mutation databases

BioMutaiLTB
DMDMi549088

Proteomic databases

PaxDbiQ06643
PeptideAtlasiQ06643
PRIDEiQ06643
ProteomicsDBi58468
58469 [Q06643-2]

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

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]

Organism-specific databases

CTDi4050
DisGeNETi4050
EuPathDBiHostDB:ENSG00000227507.2
GeneCardsiLTB
HGNCiHGNC:6711 LTB
HPAiHPA048884
MIMi600978 gene
neXtProtiNX_Q06643
OpenTargetsiENSG00000227507
PharmGKBiPA30475
GenAtlasiSearch...

Phylogenomic databases

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

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

Miscellaneous databases

ChiTaRSiLTB human
GeneWikiiLymphotoxin_beta
GenomeRNAii4050
PROiPR:Q06643
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000227507 Expressed in 161 organ(s), highest expression level in adrenal gland
CleanExiHS_LTB
ExpressionAtlasiQ06643 baseline and differential
GenevisibleiQ06643 HS

Family and domain databases

CDDicd00184 TNF, 1 hit
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
ProtoNetiSearch...

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: September 12, 2018
This is version 166 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. SIMILARITY comments
    Index of protein domains and families
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  5. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  6. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
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