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UniProtKB - Q06643 (TNFC_HUMAN)
Protein
Lymphotoxin-beta
Gene
LTB
Organism
Homo sapiens (Human)
Status
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
- cell-cell signaling Source: ProtInc
- gene expression Source: Ensembl
- immune response Source: InterPro
- lymph node development Source: Ensembl
- positive regulation of interleukin-12 production Source: UniProtKB
- signal transduction Source: ProtInc
- skin development Source: Ensembl
Keywordsi
Molecular function | Cytokine |
Enzyme and pathway databases
PathwayCommonsi | Q06643 |
Reactomei | R-HSA-5668541, TNFR2 non-canonical NF-kB pathway R-HSA-5676594, TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway |
SignaLinki | Q06643 |
SIGNORi | Q06643 |
Names & Taxonomyi
Protein namesi | Recommended name: Lymphotoxin-betaShort 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 |
Organismi | Homo sapiens (Human) |
Taxonomic identifieri | 9606 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Proteomesi |
|
Organism-specific databases
HGNCi | HGNC:6711, LTB |
MIMi | 600978, gene |
neXtProti | NX_Q06643 |
VEuPathDBi | HostDB:ENSG00000227507 |
Subcellular locationi
Other locations
- Membrane Curated; Single-pass type II membrane protein Curated
Extracellular region or secreted
- extracellular space Source: UniProtKB-KW
Plasma Membrane
- plasma membrane Source: Reactome
Other locations
- integral component of membrane Source: UniProtKB-KW
Topology
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Topological domaini | 1 – 18 | CytoplasmicSequence analysisAdd BLAST | 18 | |
Transmembranei | 19 – 48 | Helical; Signal-anchor for type II membrane proteinSequence analysisAdd BLAST | 30 | |
Topological domaini | 49 – 244 | ExtracellularSequence analysisAdd BLAST | 196 |
Keywords - Cellular componenti
MembranePathology & Biotechi
Organism-specific databases
DisGeNETi | 4050 |
OpenTargetsi | ENSG00000227507 |
PharmGKBi | PA30475 |
Miscellaneous databases
Pharosi | Q06643, Tbio |
Chemistry databases
ChEMBLi | CHEMBL3833421 |
Genetic variation databases
BioMutai | LTB |
DMDMi | 549088 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000185486 | 1 – 244 | Lymphotoxin-betaAdd BLAST | 244 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Glycosylationi | 222 | N-linked (GlcNAc...) asparagineSequence analysis | 1 |
Keywords - PTMi
GlycoproteinProteomic databases
MassIVEi | Q06643 |
PaxDbi | Q06643 |
PeptideAtlasi | Q06643 |
PRIDEi | Q06643 |
ProteomicsDBi | 58468 [Q06643-1] 58469 [Q06643-2] |
PTM databases
GlyGeni | Q06643, 1 site |
PhosphoSitePlusi | Q06643 |
Expressioni
Tissue specificityi
Spleen and thymus.
Gene expression databases
Bgeei | ENSG00000227507, Expressed in adrenal gland and 179 other tissues |
ExpressionAtlasi | Q06643, baseline and differential |
Genevisiblei | Q06643, HS |
Organism-specific databases
HPAi | ENSG00000227507, Group enriched (intestine, lymphoid tissue) |
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
- signaling receptor binding Source: ProtInc
- tumor necrosis factor receptor binding Source: InterPro
Protein-protein interaction databases
BioGRIDi | 110228, 2 interactors |
CORUMi | Q06643 |
DIPi | DIP-2996N |
IntActi | Q06643, 6 interactors |
STRINGi | 9606.ENSP00000410481 |
Miscellaneous databases
RNActi | Q06643, protein |
Family & Domainsi
Sequence similaritiesi
Belongs to the tumor necrosis factor family.Curated
Keywords - Domaini
Signal-anchor, Transmembrane, Transmembrane helixPhylogenomic databases
eggNOGi | ENOG502SMSQ, Eukaryota |
GeneTreei | ENSGT01040000240509 |
HOGENOMi | CLU_096531_0_0_1 |
InParanoidi | Q06643 |
OMAi | RPQGRGC |
PhylomeDBi | Q06643 |
TreeFami | TF337780 |
Family and domain databases
CDDi | cd00184, TNF, 1 hit |
Gene3Di | 2.60.120.40, 1 hit |
InterProi | View protein in InterPro IPR006053, TNF IPR002961, TNF_C IPR021184, TNF_CS IPR006052, TNF_dom IPR008983, Tumour_necrosis_fac-like_dom |
PANTHERi | PTHR11471:SF29, PTHR11471:SF29, 1 hit |
Pfami | View protein in Pfam PF00229, TNF, 1 hit |
PRINTSi | PR01234, TNECROSISFCT PR01237, TNFC |
SMARTi | View protein in SMART SM00207, TNF, 1 hit |
SUPFAMi | SSF49842, SSF49842, 1 hit |
PROSITEi | View protein in PROSITE PS00251, TNF_1, 1 hit PS50049, TNF_2, 1 hit |
s (2)i Sequence
Sequence statusi: Complete.
This entry describes 2 produced by isoformsialternative splicing. AlignAdd to basketIsoform 1 (identifier: Q06643-1) [UniParc]FASTAAdd to basket
This isoform has been chosen as the sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry. canonicali
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
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 60 – 69 | DPGAQAQQGL → GLSAPGSGRT in AAB37342 (PubMed:9299492).Curated | 10 |
Natural variant
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Natural variantiVAR_013025 | 70 | G → E1 PublicationCorresponds to variant dbSNP:rs3093554Ensembl. | 1 | |
Natural variantiVAR_016331 | 84 | S → R1 PublicationCorresponds to variant dbSNP:rs4647186Ensembl. | 1 | |
Natural variantiVAR_016332 | 87 | L → F1 PublicationCorresponds to variant dbSNP:rs4647187EnsemblClinVar. | 1 | |
Natural variantiVAR_013026 | 111 | A → P1 PublicationCorresponds to variant dbSNP:rs3093555Ensembl. | 1 | |
Natural variantiVAR_029145 | 122 | A → D. Corresponds to variant dbSNP:rs2229699Ensembl. | 1 |
Alternative sequence
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Alternative sequenceiVSP_006441 | 53 – 77 | GLVTE…KLPEE → GLGFRSCQRRSQKQISAPGS QLPTS in isoform 2. 3 PublicationsAdd BLAST | 25 | |
Alternative sequenceiVSP_006442 | 78 – 244 | Missing in isoform 2. 3 PublicationsAdd BLAST | 167 |
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 |
CCDSi | CCDS4703.1 [Q06643-1] CCDS4704.1 [Q06643-2] |
PIRi | A46066 JC5645 |
RefSeqi | NP_002332.1, NM_002341.1 [Q06643-1] NP_033666.1, NM_009588.1 [Q06643-2] |
Genome annotation databases
Keywords - Coding sequence diversityi
Alternative splicingSimilar 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 |
CCDSi | CCDS4703.1 [Q06643-1] CCDS4704.1 [Q06643-2] |
PIRi | A46066 JC5645 |
RefSeqi | NP_002332.1, NM_002341.1 [Q06643-1] NP_033666.1, NM_009588.1 [Q06643-2] |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
4MXW | X-ray | 3.60 | B/D/Y/Z | 86-244 | [»] | |
SMRi | Q06643 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 110228, 2 interactors |
CORUMi | Q06643 |
DIPi | DIP-2996N |
IntActi | Q06643, 6 interactors |
STRINGi | 9606.ENSP00000410481 |
Chemistry databases
ChEMBLi | CHEMBL3833421 |
PTM databases
GlyGeni | Q06643, 1 site |
PhosphoSitePlusi | Q06643 |
Genetic variation databases
BioMutai | LTB |
DMDMi | 549088 |
Proteomic databases
MassIVEi | Q06643 |
PaxDbi | Q06643 |
PeptideAtlasi | Q06643 |
PRIDEi | Q06643 |
ProteomicsDBi | 58468 [Q06643-1] 58469 [Q06643-2] |
Protocols and materials databases
ABCDi | Q06643, 8 sequenced antibodies |
Antibodypediai | 27204, 205 antibodies from 25 providers |
DNASUi | 4050 |
Genome annotation databases
Organism-specific databases
CTDi | 4050 |
DisGeNETi | 4050 |
GeneCardsi | LTB |
HGNCi | HGNC:6711, LTB |
HPAi | ENSG00000227507, Group enriched (intestine, lymphoid tissue) |
MIMi | 600978, gene |
neXtProti | NX_Q06643 |
OpenTargetsi | ENSG00000227507 |
PharmGKBi | PA30475 |
VEuPathDBi | HostDB:ENSG00000227507 |
GenAtlasi | Search... |
Phylogenomic databases
eggNOGi | ENOG502SMSQ, Eukaryota |
GeneTreei | ENSGT01040000240509 |
HOGENOMi | CLU_096531_0_0_1 |
InParanoidi | Q06643 |
OMAi | RPQGRGC |
PhylomeDBi | Q06643 |
TreeFami | TF337780 |
Enzyme and pathway databases
PathwayCommonsi | Q06643 |
Reactomei | R-HSA-5668541, TNFR2 non-canonical NF-kB pathway R-HSA-5676594, TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway |
SignaLinki | Q06643 |
SIGNORi | Q06643 |
Miscellaneous databases
BioGRID-ORCSi | 4050, 5 hits in 1035 CRISPR screens |
ChiTaRSi | LTB, human |
GeneWikii | Lymphotoxin_beta |
GenomeRNAii | 4050 |
Pharosi | Q06643, Tbio |
PROi | PR:Q06643 |
RNActi | Q06643, protein |
SOURCEi | Search... |
Gene expression databases
Bgeei | ENSG00000227507, Expressed in adrenal gland and 179 other tissues |
ExpressionAtlasi | Q06643, baseline and differential |
Genevisiblei | Q06643, HS |
Family and domain databases
CDDi | cd00184, TNF, 1 hit |
Gene3Di | 2.60.120.40, 1 hit |
InterProi | View protein in InterPro IPR006053, TNF IPR002961, TNF_C IPR021184, TNF_CS IPR006052, TNF_dom IPR008983, Tumour_necrosis_fac-like_dom |
PANTHERi | PTHR11471:SF29, PTHR11471:SF29, 1 hit |
Pfami | View protein in Pfam PF00229, TNF, 1 hit |
PRINTSi | PR01234, TNECROSISFCT PR01237, TNFC |
SMARTi | View protein in SMART SM00207, TNF, 1 hit |
SUPFAMi | SSF49842, SSF49842, 1 hit |
PROSITEi | View protein in PROSITE PS00251, TNF_1, 1 hit PS50049, TNF_2, 1 hit |
MobiDBi | Search... |
Entry informationi
Entry namei | TNFC_HUMAN | |
Accessioni | Q06643Primary (citable) accession number: Q06643 Secondary accession number(s): P78370, Q52LU8, Q99761 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | June 1, 1994 |
Last sequence update: | June 1, 1994 | |
Last modified: | February 23, 2022 | |
This is version 187 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program | |
Disclaimer | Any 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, Direct protein sequencing, Reference proteomeDocuments
- Human chromosome 6
Human chromosome 6: entries, gene names and cross-references to MIM - Human entries with genetic variants
List of human entries with genetic variants - Human variants curated from literature reports
Index of human variants curated from literature reports - 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