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501  structures 3076  species 33  interactions 138558  sequences 6438  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. Of the three fibronectin-type domains, type III is the only one without disulfide bonding present. Fibronectin domains are found in a wide variety of extracellular proteins. They are widely distributed in animal species, but also found 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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Pfam Clan

This family is a member of clan E-set (CL0159), which has the following description:

This clan includes a diverse range of domains that have an Ig-like fold and appear to be distantly related to each other. The clan includes: PKD domains, cadherins and several families of bacterial Ig-like domains as well as viral tail fibre proteins. it also includes several Fibronectin type III domain-containing families.

The clan contains the following 218 members:

A2M A2M_BRD A2M_recep Adeno_GP19K AlcCBM31 Alpha-amylase_N Alpha_adaptinC2 Alpha_E2_glycop Arch_flagellin Arylsulfotran_N ASF1_hist_chap ATG19_autophagy BACON Big_1 Big_10 Big_11 Big_2 Big_3 Big_3_2 Big_3_3 Big_3_5 Big_4 Big_5 Big_6 Big_7 Big_8 Big_9 Bile_Hydr_Trans BiPBP_C bMG1 bMG10 bMG3 bMG5 bMG6 BslA BsuPI Cadherin Cadherin-like Cadherin_2 Cadherin_3 Cadherin_4 Cadherin_5 Cadherin_pro CagX Calx-beta Candida_ALS_N CARDB CBM39 CBM_X2 CD45 CelD_N Ceramidse_alk_C CHB_HEX_C CHB_HEX_C_1 ChitinaseA_N ChiW_Ig_like CHU_C Coatamer_beta_C COP-gamma_platf CopC Cyc-maltodext_N Cytomega_US3 DsbC DUF11 DUF1410 DUF1425 DUF1929 DUF2271 DUF3244 DUF3327 DUF3416 DUF3458 DUF3501 DUF3823_C DUF3859 DUF3872 DUF4165 DUF4179 DUF4426 DUF4448 DUF4469 DUF4625 DUF4879 DUF4981 DUF4982 DUF5001 DUF5008 DUF5011 DUF5065 DUF5115 DUF525 DUF5643 DUF916 EB_dh ECD EpoR_lig-bind ERAP1_C EstA_Ig_like Filamin FixG_C Flavi_glycop_C FlgD_ig fn3 Fn3-like fn3_2 fn3_4 fn3_5 fn3_6 FN3_7 Fn3_assoc fn3_PAP GBS_Bsp-like Glucodextran_B Glyco_hydro2_C5 Glyco_hydro_2 Glyco_hydro_61 Gmad2 GMP_PDE_delta GPI-anchored Hanta_G1 He_PIG He_PIG_assoc HECW_N HemeBinding_Shp Hemocyanin_C Herpes_BLLF1 HYR IFNGR1 Ig_GlcNase Ig_mannosidase IL12p40_C Il13Ra_Ig IL17R_fnIII_D1 IL17R_fnIII_D2 IL2RB_N1 IL3Ra_N IL4Ra_N IL6Ra-bind Inhibitor_I42 Inhibitor_I71 Integrin_alpha2 Interfer-bind Invasin_D3 IRK_C IrmA Iron_transport LEA_2 Lep_receptor_Ig LIFR_N Lipase_bact_N LPMO_10 LRR_adjacent LTD Mannosidase_ig MG1 MG2 MG3 MG4 Mo-co_dimer N_BRCA1_IG Na_K-ATPase NEAT Neocarzinostat Neurexophilin NPCBM_assoc PapD_C PBP-Tp47_c Peptidase_C25_C Phlebovirus_G2 PhoD_N PKD PKD_2 PKD_3 Pollen_allerg_1 Pox_vIL-18BP Pur_ac_phosph_N Qn_am_d_aII Qn_am_d_aIII RabGGT_insert Reeler REJ RET_CLD1 RET_CLD3 RET_CLD4 RGI_lyase RHD_dimer Rho_GDI Rib SCAB-Ig SKICH SLAM SoxZ SprB SusE SVA SWM_repeat T2SS-T3SS_pil_N Tafi-CsgC TarS_C1 TcA_RBD TcfC TIG TIG_2 TIG_plexin Tissue_fac Top6b_C Transglut_C Transglut_N TRAP_beta Tuberculin UL16 Velvet WIF Wzt_C Y_Y_Y YBD ZirS_C Zona_pellucida

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
(138558)
Representative proteomes UniProt
(231114)
NCBI
(663930)
Meta
(1606)
RP15
(22770)
RP35
(50709)
RP55
(86895)
RP75
(106318)
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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
(138558)
Representative proteomes UniProt
(231114)
NCBI
(663930)
Meta
(1606)
RP15
(22770)
RP35
(50709)
RP55
(86895)
RP75
(106318)
Alignment:
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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
(138558)
Representative proteomes UniProt
(231114)
NCBI
(663930)
Meta
(1606)
RP15
(22770)
RP35
(50709)
RP55
(86895)
RP75
(106318)
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
Sequence Ontology: SO:0000417
Author: Sonnhammer ELL
Number in seed: 98
Number in full: 138558
Average length of the domain: 84.90 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 21.86 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 25.0 25.0
Noise cut-off 24.9 24.9
Model length: 85
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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

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Interactions

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

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

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 501 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 sequence.

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