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192  structures 145  species 6  interactions 2849  sequences 99  architectures

Family: TNFR_c6 (PF00020)

Summary: TNFR/NGFR cysteine-rich region

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This is the Wikipedia entry entitled "Tumor necrosis factor receptor". More...

Tumor necrosis factor receptor Edit Wikipedia article

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TNFR/NGFR cysteine-rich region Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001368

A number of proteins, some of which are known to be receptors for growth factors, have been found to contain a cysteine-rich domain of about 110 to 160 amino acids in their N-terminal part, that can be subdivided into four (or in some cases, three) modules of about 40 residues containing 6 conserved cysteines. Some of the proteins containing this domain are listed below [PUBMED:2174582, PUBMED:15335933, PUBMED:15335677]:

  • Tumor Necrosis Factor type I and type II receptors (TNFR). Both receptors bind TNF-alpha and TNF-beta, but are only similar in the cysteine-rich region
  • Shope fibroma virus soluble TNF receptor (protein T2)
  • Lymphotoxin alpha/beta receptor
  • Low-affinity nerve growth factor receptor (LA-NGFR) (p75)
  • CD40 (Bp50), the receptor for the CD40L (or TRAP) cytokine
  • CD27, the receptor for the CD27L cytokine
  • CD30, the receptor for the CD30L cytokine
  • T-cell protein 4-1BB, the receptor for the 4-1BBL putative cytokine
  • FAS antigen (or APO-1), the receptor for FASL, a protein involved in apoptosis (programmed cell death)
  • T-cell antigen OX40, the receptor for the OX40L cytokine
  • Wsl-1, a receptor (for a yet undefined ligand) that mediates apoptosis
  • Vaccinia virus protein A53 (SalF19R)

It has been shown [PUBMED:8387891] that the six cysteines all involved in intrachain disulphide bonds. A schematic representation of the structure of the 40 residue module of these receptors is shown below:

                  +-------------+    +--------------+
                  |             |    |              |
                 xCxxxxxxxxxxxxxCxCxxCxxxxxxxxxCxxxxCxx
                                  |            |
                                  +------------+
'C': conserved cysteine involved in a disulphide bond.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan TNF_receptor (CL0607), which has the following description:

The clan contains the following 4 members:

BaffR-Tall_bind BCMA-Tall_bind TACI-CRD2 TNFR_c6

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(630)
Full
(2849)
Representative proteomes UniProt
(5360)
NCBI
(11676)
Meta
(66)
RP15
(685)
RP35
(1019)
RP55
(1786)
RP75
(2447)
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PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(630)
Full
(2849)
Representative proteomes UniProt
(5360)
NCBI
(11676)
Meta
(66)
RP15
(685)
RP35
(1019)
RP55
(1786)
RP75
(2447)
Alignment:
Format:
Order:
Sequence:
Gaps:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(630)
Full
(2849)
Representative proteomes UniProt
(5360)
NCBI
(11676)
Meta
(66)
RP15
(685)
RP35
(1019)
RP55
(1786)
RP75
(2447)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Swissprot_feature_table
Previous IDs: none
Type: Domain
Author: Sonnhammer ELL
Number in seed: 630
Number in full: 2849
Average length of the domain: 39.70 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 15.41 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 20.6
Trusted cut-off 27.0 20.6
Noise cut-off 26.9 20.5
Model length: 39
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Interactions

There are 6 interactions for this family. More...

Ig_2 TNFR_c6 TNF NGF TNF NGF

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the TNFR_c6 domain has been found. There are 192 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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