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392  structures 1148  species 33  interactions 65361  sequences 3581  architectures

Family: fn3 (PF00041)

Summary: Fibronectin type III domain

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This is the Wikipedia entry entitled "Fibronectin type III domain". More...

Fibronectin type III domain Edit Wikipedia article

Fibronectin type III domain
PDB 1ttg EBI.jpg
The tenth type III domain of fibronectin
Identifiers
Symbol fn3
Pfam PF00041
Pfam clan CL0159
InterPro IPR003961
SMART FN3
PROSITE PDOC00214
SCOP 1ttf
SUPERFAMILY 1ttf
CDD cd00063

The Fibronectin type III domain is an evolutionary conserved protein domain that is widely found in animal proteins. The fibronectin protein in which this domain was first identified contains 16 copies of this domain. The domain is about 100 amino acids long and possesses a beta sandwich structure. Fibronectin domains are found in a wide variety of extracellular proteins. They are widely distributed in animal species, but also found more sporadically in yeast, plant and bacterial proteins.

Human proteins containing this domain

ABI3BP; ANKFN1; ASTN2; AXL; BOC; BZRAP1; C20orf75; CDON; CHL1; CMYA5; CNTFR; CNTN1; CNTN2; CNTN3; CNTN4; CNTN5; CNTN6; COL12A1; COL14A1; COL20A1; COL7A1; CRLF1; CRLF3; CSF2RB; CSF3R; DCC; DSCAM; DSCAML1; EBI3; EGFLAM; EPHA1; EPHA10; EPHA2; EPHA3; EPHA4; EPHA5; EPHA6; EPHA7; EPHA8; EPHB1; EPHB2; EPHB3; EPHB4; EPHB6; EPOR; FANK1; FLRT1; FLRT2; FLRT3; FN1; FNDC1; FNDC3A; FNDC3B; FNDC4; FNDC5; FNDC7; FNDC8; FSD1; FSD1L; FSD2; GHR; HCFC1; HCFC2; HUGO; IFNGR2; IGF1R; IGSF22; IGSF9; IGSF9B; IL4R; IL11RA; IL12B; IL12RB1; IL12RB2; IL20RB; IL23R; IL27RA; IL31RA; IL6R; IL6ST; IL7R; INSR; INSRR; ITGB4; Il6ST; KAL1; KALRN; L1CAM; LEPR; LIFR; LRFN2; LRFN3; LRFN4; LRFN5; LRIT1; LRRN1; LRRN3; MERTK; MID1; MID2; MPL; MYBPC1; MYBPC2; MYBPC3; MYBPH; MYBPHL; MYLK; MYOM1; MYOM2; MYOM3; NCAM1; NCAM2; NEO1; NFASC; NOPE; NPHS1; NRCAM; OBSCN; OBSL1; OSMR; PHYHIP; PHYHIPL; PRLR; PRODH2; PTPRB; PTPRC; PTPRD; PTPRF; PTPRG; PTPRH; PTPRJ; PTPRK; PTPRM; PTPRO; PTPRS; PTPRT; PTPRU; PTPRZ1; PTPsigma; PUNC; RIMBP2; ROBO1; ROBO2; ROBO3; ROBO4; ROS1; SDK1; SDK2; SNED1; SORL1; SPEG; TEK; TIE1; TNC; TNN; TNR; TNXB; TRIM36; TRIM42; TRIM46; TRIM67; TRIM9; TTN; TYRO3; UMODL1; USH2A; VASN; VWA1; dJ34F7.1; fmi;

See also

  • Monobody, an engineered antibody mimetic based on the structure of the fibronectin type III domain

References

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Fibronectin type III domain Provide feedback

No Pfam abstract.

Literature references

  1. Bazan JF; , PNAS USA 1990;87:6934-6938.: Structural design and molecular evolution of a cytokine receptor superfamily. PUBMED:2169613 EPMC:2169613

  2. Little E, Bork P, Doolittle R; , J Mol Evol 1994;39:631-643.: Tracing the spread of fibronectin type III domains in bacterial glycohydrolases. PUBMED:7528812 EPMC:7528812

  3. Kornblihtt AR, Umezawa K, Vibe-Pedersen K, Baralle FE; , EMBO J 1985;4:1755-1759.: Primary structure of human fibronectin: differential splicing may generate at least 10 polypeptides from a single gene. PUBMED:2992939 EPMC:2992939


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003961

Fibronectin is a dimeric glycoprotein composed of disulfide-linked subunits with a molecular weight of 220-250 kDa each. It is involved in cell adhesion, cell morphology, thrombosis, cell migration, and embryonic differentiation. Fibronectin is a modular protein composed of homologous repeats of three prototypical types of domains known as types I, II, and III [PUBMED:6218503].

Fibronectin type-III (FN3) repeats are both the largest and the most common of the fibronectin subdomains. Domains homologous to FN3 repeats have been found in various animal protein families including other extracellular-matrix molecules, cell-surface receptors, enzymes, and muscle proteins [PUBMED:1409594]. Structures of individual FN3 domains have revealed a conserved beta sandwich fold with one beta sheet containing four strands and the other sheet containing three strands (see for example {PDB:1TEN}) [PUBMED:1279805]. This fold is topologically very similar to that of Ig-like domains, with a notable difference being the lack of a conserved disulfide bond in FN3 domains. Distinctive hydrophobic core packing and the lack of detectable sequence homology between immunoglobulin and FN3 domains suggest, however, that these domains are not evolutionarily related [PUBMED:1279805].

FN3 exhibits functional as well as structural modularity. Sites of interaction with other molecules have been mapped to short stretch of amino acids such as the Arg-Gly-Asp (RGD) sequence found in various FN3 domains. The RGD sequences is involved in interactions with integrin. Small peptides containing the RGD sequence can modulate a variety of cell adhesion invents associated with thrombosis, inflammation, and tumor metastasis. These properties have led to the investigation of RGD peptides and RGD peptide analogs as potential therapeutic agents [PUBMED:8548820].

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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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
(98)
Full
(65361)
Representative proteomes UniProt
(126149)
NCBI
(388753)
Meta
(1702)
RP15
(13106)
RP35
(23985)
RP55
(41587)
RP75
(55683)
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PP/heatmap 1                

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

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

Format an alignment

  Seed
(98)
Full
(65361)
Representative proteomes UniProt
(126149)
NCBI
(388753)
Meta
(1702)
RP15
(13106)
RP35
(23985)
RP55
(41587)
RP75
(55683)
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
(98)
Full
(65361)
Representative proteomes UniProt
(126149)
NCBI
(388753)
Meta
(1702)
RP15
(13106)
RP35
(23985)
RP55
(41587)
RP75
(55683)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download     Download  
Gzipped 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: 98
Number in full: 65361
Average length of the domain: 84.90 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 22.81 %

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 24.5 24.5
Trusted cut-off 24.5 24.5
Noise cut-off 24.4 24.4
Model length: 85
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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Interactions

There are 33 interactions for this family. More...

Hormone_1 IL6 CH EpoR_lig-bind Pkinase Pectate_lyase_3 EPO_TPO Hormone_recep HH_signal RGM_C Hormone_1 V-set EPO_TPO MatE ig Glyco_hydro_28 IL6Ra-bind Glyco_hydro_28 HH_signal I-set IL2 RGM_N IL4 EpoR_lig-bind I-set IL15 IL7 fn3 Lectin_C Lipocalin Ig_2 IL2 LIF_OSM

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 fn3 domain has been found. There are 392 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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