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Q06643 (TNFC_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 139. 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:
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 names
Name:LTB
Synonyms:TNFC, TNFSF3
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length244 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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.

Subunit structure

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

Subcellular location

Membrane; Single-pass type II membrane protein Potential.

Tissue specificity

Spleen and thymus.

Sequence similarities

Belongs to the tumor necrosis factor family.

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q06643-1)

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.
Isoform 2 (identifier: Q06643-2)

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 244244Lymphotoxin-beta
PRO_0000185486

Regions

Topological domain1 – 1818Cytoplasmic Potential
Transmembrane19 – 4830Helical; Signal-anchor for type II membrane protein; Potential
Topological domain49 – 244196Extracellular Potential

Amino acid modifications

Glycosylation2221N-linked (GlcNAc...) Potential

Natural variations

Alternative sequence53 – 7725GLVTE…KLPEE → GLGFRSCQRRSQKQISAPGS QLPTS in isoform 2.
VSP_006441
Alternative sequence78 – 244167Missing in isoform 2.
VSP_006442
Natural variant701G → E. Ref.6
Corresponds to variant rs3093554 [ dbSNP | Ensembl ].
VAR_013025
Natural variant841S → R. Ref.7
Corresponds to variant rs4647186 [ dbSNP | Ensembl ].
VAR_016331
Natural variant871L → F. Ref.7
Corresponds to variant rs4647187 [ dbSNP | Ensembl ].
VAR_016332
Natural variant1111A → P. Ref.6
Corresponds to variant rs3093555 [ dbSNP | Ensembl ].
VAR_013026
Natural variant1221A → D.
Corresponds to variant rs2229699 [ dbSNP | Ensembl ].
VAR_029145

Experimental info

Sequence conflict60 – 6910DPGAQAQQGL → GLSAPGSGRT in AAB37342. Ref.2

Sequences

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

Last modified June 1, 1994. Version 1.
Checksum: F41569459830ED4C

FASTA24425,390
        10         20         30         40         50         60 
MGALGLEGRG GRLQGRGSLL LAVAGATSLV TLLLAVPITV LAVLALVPQD QGGLVTETAD 

        70         80         90        100        110        120 
PGAQAQQGLG FQKLPEEEPE TDLSPGLPAA HLIGAPLKGQ GLGWETTKEQ AFLTSGTQFS 

       130        140        150        160        170        180 
DAEGLALPQD GLYYLYCLVG YRGRAPPGGG DPQGRSVTLR SSLYRAGGAY GPGTPELLLE 

       190        200        210        220        230        240 
GAETVTPVLD PARRQGYGPL WYTSVGFGGL VQLRRGERVY VNISHPDMVD FARGKTFFGA 


VMVG 

« Hide

Isoform 2 [UniParc].

Checksum: 8F1256D793D85397
Show »

FASTA777,780

References

« Hide 'large scale' references
[1]"Lymphotoxin beta, a novel member of the TNF family that forms a heteromeric complex with lymphotoxin on the cell surface."
Browning J.L., Ngam-Ek A., Lawton P., Demarinis J., Tizard R., Chow E.P., Hession C., O'Brine-Greco B., Foley S.F., Ware C.F.
Cell 72:847-856(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE (ISOFORM 1), PARTIAL PROTEIN SEQUENCE.
Tissue: T-cell.
[2]"Identification of two lymphotoxin beta isoforms expressed in human lymphoid cell lines and non-Hodgkin's lymphomas."
Warzocha K., Renard N., Charlot C., Bienvenu J., Coiffier B., Salles G.
Biochem. Biophys. Res. Commun. 238:273-276(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2).
[3]"A new member of the Ig superfamily and a V-ATPase G subunit are among the predicted products of novel genes close to the TNF locus in the human MHC."
Neville M.J., Campbell R.D.
J. Immunol. 162:4745-4754(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE (ISOFORM 1).
[4]"Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse."
Xie T., Rowen L., Aguado B., Ahearn M.E., Madan A., Qin S., Campbell R.D., Hood L.
Genome Res. 13:2621-2636(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"Homo sapiens 2,229,817bp genomic DNA of 6p21.3 HLA class I region."
Shiina S., Tamiya G., Oka A., Inoko H.
Submitted (SEP-1999) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]SeattleSNPs variation discovery resource
Submitted (DEC-2001) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANTS GLU-70 AND PRO-111.
[7]NIEHS SNPs program
Submitted (JAN-2003) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANTS ARG-84 AND PHE-87.
[8]"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).
Tissue: Spleen.
[9]Mural R.J., Istrail S., Sutton G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[10]"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] (ISOFORMS 1 AND 2).
Tissue: Colon.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRA46066.
JC5645.
RefSeqNP_002332.1. NM_002341.1.
NP_033666.1. NM_009588.1.
UniGeneHs.376208.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4MXWX-ray3.60B/D/Y/Z86-244[»]
ProteinModelPortalQ06643.
SMRQ06643. Positions 87-243.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid110228. 2 interactions.
DIPDIP-2996N.
IntActQ06643. 5 interactions.
STRING9606.ENSP00000393693.

Chemistry

DrugBankDB00065. Infliximab.
DB00641. Simvastatin.

Polymorphism databases

DMDM549088.

Proteomic databases

PaxDbQ06643.
PRIDEQ06643.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000376117; 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]
GeneID4050.
KEGGhsa:4050.
UCSCuc003nuk.3. human. [Q06643-1]
uc003nul.3. human. [Q06643-2]

Organism-specific databases

CTD4050.
GeneCardsGC06M031549.
GC06Mi31559.
GC06Mj31535.
GC06Mk31530.
GC06Ml31587.
GC06Mm31624.
GC06Mn31538.
GC06Mo31538.
HGNCHGNC:6711. LTB.
HPAHPA048884.
MIM600978. gene.
neXtProtNX_Q06643.
PharmGKBPA30475.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG44178.
HOGENOMHOG000273916.
HOVERGENHBG000209.
InParanoidQ06643.
KOK03157.
OMAREYGPLW.
OrthoDBEOG7V4B0Q.
PhylomeDBQ06643.
TreeFamTF337780.

Gene expression databases

ArrayExpressQ06643.
BgeeQ06643.
CleanExHS_LTB.
GenevestigatorQ06643.

Family and domain databases

Gene3D2.60.120.40. 1 hit.
InterProIPR006053. TNF.
IPR002961. TNF_C.
IPR021184. TNF_CS.
IPR006052. TNF_dom.
IPR008983. Tumour_necrosis_fac-like_dom.
[Graphical view]
PfamPF00229. TNF. 1 hit.
[Graphical view]
PRINTSPR01234. TNECROSISFCT.
PR01237. TNFC.
SMARTSM00207. TNF. 1 hit.
[Graphical view]
SUPFAMSSF49842. SSF49842. 1 hit.
PROSITEPS00251. TNF_1. 1 hit.
PS50049. TNF_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSLTB. human.
GeneWikiLymphotoxin_beta.
GenomeRNAi4050.
NextBio15864.
PROQ06643.
SOURCESearch...

Entry information

Entry nameTNFC_HUMAN
AccessionPrimary (citable) accession number: Q06643
Secondary accession number(s): P78370, Q52LU8, Q99761
Entry history
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: June 1, 1994
Last modified: March 19, 2014
This is version 139 of the entry and version 1 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

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 6

Human chromosome 6: entries, gene names and cross-references to MIM