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65  structures 258  species 0  interactions 1053  sequences 87  architectures

Family: I-EGF_1 (PF18372)

Summary: Integrin beta epidermal growth factor like domain 1

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Integrin beta epidermal growth factor like domain 1 Provide feedback

This is the I-EGF 1 domain found in several integrin betas such as integrin beta 1-7. Structural analysis reveal an epidermal growth factor-like (I-EGF) domains 1 and 2 [1]. EGF1 lacks one disulfide (C2-C4) relative to the integrin EGF 2, 3, and 4 domains, this allows the C-terminal end of EGF1 to flex remarkably relative to its N-terminal end [14].

Literature references

  1. Dong X, Hudson NE, Lu C, Springer TA;, Nat Struct Mol Biol. 2014;21:1091-1096.: Structural determinants of integrin beta-subunit specificity for latent TGF-beta. PUBMED:25383667 EPMC:25383667

  2. Xiong JP, Stehle T, Diefenbach B, Zhang R, Dunker R, Scott DL, Joachimiak A, Goodman SL, Arnaout MA;, Science. 2001;294:339-345.: Crystal structure of the extracellular segment of integrin alpha Vbeta3. PUBMED:11546839 EPMC:11546839

  3. Xiong JP, Stehle T, Zhang R, Joachimiak A, Frech M, Goodman SL, Arnaout MA;, Science. 2002;296:151-155.: Crystal structure of the extracellular segment of integrin alpha Vbeta3 in complex with an Arg-Gly-Asp ligand. PUBMED:11884718 EPMC:11884718

  4. Xiong JP, Stehle T, Goodman SL, Arnaout MA;, J Biol Chem. 2004;279:40252-40254.: A novel adaptation of the integrin PSI domain revealed from its crystal structure. PUBMED:15299032 EPMC:15299032

  5. Springer TA, Zhu J, Xiao T;, J Cell Biol. 2008;182:791-800.: Structural basis for distinctive recognition of fibrinogen gammaC peptide by the platelet integrin alphaIIbbeta3. PUBMED:18710925 EPMC:18710925

  6. Zhu J, Luo BH, Xiao T, Zhang C, Nishida N, Springer TA;, Mol Cell. 2008;32:849-861.: Structure of a complete integrin ectodomain in a physiologic resting state and activation and deactivation by applied forces. PUBMED:19111664 EPMC:19111664

  7. Xiong JP, Mahalingham B, Alonso JL, Borrelli LA, Rui X, Anand S, Hyman BT, Rysiok T, Muller-Pompalla D, Goodman SL, Arnaout MA;, J Cell Biol. 2009;186:589-600.: Crystal structure of the complete integrin alphaVbeta3 ectodomain plus an alpha/beta transmembrane fragment. PUBMED:19704023 EPMC:19704023

  8. Zhu J, Zhu J, Negri A, Provasi D, Filizola M, Coller BS, Springer TA;, Blood. 2010;116:5050-5059.: Closed headpiece of integrin alphaIIbbeta3 and its complex with an alphaIIbbeta3-specific antagonist that does not induce opening. PUBMED:20679525 EPMC:20679525

  9. Zhu J, Choi WS, McCoy JG, Negri A, Zhu J, Naini S, Li J, Shen M, Huang W, Bougie D, Rasmussen M, Aster R, Thomas CJ, Filizola M, Springer TA, Coller BS;, Sci Transl Med. 2012;4:125ra32.: Structure-guided design of a high-affinity platelet integrin alphaIIbbeta3 receptor antagonist that disrupts Mg(2)(+) binding to the MIDAS. PUBMED:22422993 EPMC:22422993

  10. Zhu J, Zhu J, Springer TA;, J Cell Biol. 2013;201:1053-1068.: Complete integrin headpiece opening in eight steps. PUBMED:23798730 EPMC:23798730

  11. Choi WS, Rice WJ, Stokes DL, Coller BS;, Blood. 2013;122:4165-4171.: Three-dimensional reconstruction of intact human integrin alphaIIbbeta3: new implications for activation-dependent ligand binding. PUBMED:24136164 EPMC:24136164

  12. Dong X, Mi LZ, Zhu J, Wang W, Hu P, Luo BH, Springer TA;, Biochemistry. 2012;51:8814-8828.: alpha(V)beta(3) integrin crystal structures and their functional implications. PUBMED:23106217 EPMC:23106217

  13. Van Agthoven JF, Xiong JP, Alonso JL, Rui X, Adair BD, Goodman SL, Arnaout MA;, Nat Struct Mol Biol. 2014;21:383-388.: Structural basis for pure antagonism of integrin alphaVbeta3 by a high-affinity form of fibronectin. PUBMED:24658351 EPMC:24658351

  14. Sen M, Springer TA;, Proc Natl Acad Sci U S A. 2016;113:2940-2945.: Leukocyte integrin alphaLbeta2 headpiece structures: The alphaI domain, the pocket for the internal ligand, and concerted movements of its loops. PUBMED:26936951 EPMC:26936951


Internal database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

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 EGF (CL0001), which has the following description:

Members of this clan all belong to the EGF superfamily. This particular superfamily is characterised as having least 6 cysteine residues. These cysteines form disulphide bonds, in the order 1-3, 2-4, 5-6, which are essential for the stability of the EGF fold. These disulphide bonds are stacked in a ladder-like arrangement. The Laminin EGF family is distinguished by having an an additional disulphide bond. The function of the domains within this family remains unclear, but they are thought to largely perform a structural role. More often than not, these domains are arranged in tandem repeats in extracellular proteins.

The clan contains the following 21 members:

cEGF CFC DSL EGF EGF_2 EGF_3 EGF_alliinase EGF_CA EGF_MSP1_1 EGF_Tenascin Fibrillin_U_N FOLN FXa_inhibition Gla hEGF I-EGF_1 Laminin_EGF Plasmod_Pvs28 Sushi Sushi_2 Tme5_EGF_like

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...

View options

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
(145)
Full
(1053)
Representative proteomes UniProt
(1654)
NCBI
(3277)
Meta
(0)
RP15
(179)
RP35
(388)
RP55
(738)
RP75
(887)
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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
(145)
Full
(1053)
Representative proteomes UniProt
(1654)
NCBI
(3277)
Meta
(0)
RP15
(179)
RP35
(388)
RP55
(738)
RP75
(887)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

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
(145)
Full
(1053)
Representative proteomes UniProt
(1654)
NCBI
(3277)
Meta
(0)
RP15
(179)
RP35
(388)
RP55
(738)
RP75
(887)
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

This family is new in this Pfam release.

Seed source: ECOD:EUF04729
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: El-Gebali S
Number in seed: 145
Number in full: 1053
Average length of the domain: 29.50 aa
Average identity of full alignment: 45 %
Average coverage of the sequence by the domain: 3.32 %

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 26.1 26.1
Trusted cut-off 26.1 26.1
Noise cut-off 26.0 26.0
Model length: 29
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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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 I-EGF_1 domain has been found. There are 65 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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