Summary
The entry for 4BJ3 on the web pages of RCS Protein Data Bank contains information regarding a “collagen-like, GFOGER peptide” (authors’ words) that is at the best misleading and at the worst incorrect. This peptide is totally artificial, designed to have the integrin binding motif, GFOGER, flanked by model collagen GPP repeats so that it adopts a triple helical structure. The web page editors (I presume) have presented it as a mutated form of the α1 chain of collagen type XXVI, presumably because it scored highest in a sequence alignment. However the alignment is clearly on the basis of the GPP repeats, and this collagen has two mismatches in the key integrin GFOGER motif, specifically in the functionally important F and E residues. It is clear from the literature that the peptide was designed to study the interaction occurring in the integrin-binding collagens type I, II and IV — indeed collagen type XXVI was unknown at the time of design.
Collagen type XXVI completely lacks the GFOGER motif or any similar motif that has been shown to bind integrins. Although the possibility cannot be excluded without experimental evidence, the assumption would be that collagen type XXVI does not bind integrin α2.
The GFOGER peptide is not derived from collagen type XXVI
The PDB structure 4BJ3 is described in a file that can be downloaded from the RCS Protein Data Bank, and in the associated publication. According to these sources it consists of domain I of integrin α2 (residues 171–368) in a complex with a triple-helical “collagen-like, GFOGER peptide” of sequence [GPO]2GFOGER[GPO]3, where O represents hydroxyproline.
The web page for this structure at the RCS Protein Data Bank allows one to view the protein, and contains additional information, prepared by the site curators and web editors. This includes a “Protein Feature View” in which the GFOGER peptide is aligned to Uniprot entry Q96A83, the conceptual translation of the α1 chain of collagen type XXVI:
This is the section that the poster appears to have found, and from which he has produced an alignment that includes X, which is actually the hydroproline in the synthetic peptide. Here this is replaced by P.

I have annotated the alignment to emphasize the GFOGER region and the differences (broken circles). Of the three mismatches, two are in the crucial GFOGER region which is the basis of the interaction between collagen and integrin, and both (‘F’ and ‘E’) are at critical positions.
It is clear that the choice of alignment with collagen type XXVI is not based on anything originating from the authors and makes no biological sense. How did it arise?
I have conducted Blast searches with the sequence of the synthetic peptide and found no exact hit. The highest scoring hit is with type XXVI, even though an intelligent scoring system would have demanded perfect alignment with the GFOGER motif. I assume that a person with an informatics background, but unfamiliar with the biology, accepted this.
It is misleading and wrong!
What is the GFOGER peptide derived from?
To answer this question I tracked back through the literature, following the references in the Introduction or Methods sections, starting from the 2013 paper and ending in 1986. To summarize:
- 1986: Collagens Type I, II and IV bind to a platelet membrane adhesion protein (Cell 46, 913-920) — Subsequently this was designated VLA-2 and later integrin α2β1.
- 1994: Artificial collagen-like peptide crystalized, confirming the triple-helix that had been proposed in the 1950s (Science 266, 75–81).
- 1994: Domain I of integrin α2β1 shown to contain binding site(s) for collagen.
- 1997: Domain I of integrin α2β1 crystalized (J.Biol.Chem. 272, 28512–28517). Molecular modelling suggested that a glutamic acid side chain (E) from collagen could coordinate to the integrin through a metal ion'
- 2000: Crystal structure of a complex between domain I of integrin α2β1 and the “GFOGER peptide” (Cell, 101, 47–56). The rationale for the synthesis of this peptide is clearly stated: “…We therefore designed the shortest peptide that would fold into a stable triple helix and that had the glutamate at its center. We synthesized a 21-residue peptide with the sequence [Ac-(GPO)2GFOGER(GPO)3-NH2]
and showed that it folds into a triple helix…”
There are further papers that could be cited, but this makes the provenance of the peptide clear, as also its relationship to collagens I, II and IV. The date of 2000 for the description of this peptide is also significant given the fact that collagen XXVI was not reported until 2002 (J.Biol.Chem. 277, 37678–37684).
Nevertheless could collagen XXVI still bind integrins?
I know of no direct experiments on this topic. What I have done is to perform Blast searches with those hexapeptides that have been shown to interact with integrin, with or without activation of the later. The results were:
Peptide |
Integrin |
GFOGER |
Type I (α1 |
GFOGER |
Type II (α1) |
GFOGER |
Type IV (α3,α4,α5) |
GFOGER |
Type VII (α1) |
GFOGER |
Type XI (α1, α2) |
GLOGER |
Type I (α1,α2) |
GLOGER |
Type II (α1) |
GLOGER |
Type VII (α1) |
GASGER |
Type I (α1) |
GASGER |
Type XXIII (α1) |
GMOGER |
Type I (α1) |
GMOGER |
Type II (α1) |
GMOGER |
Type III (α1) |
GMOGER |
Type IV (α6) |
GMOGER |
Type V (α2) |
GMOGER |
Type IX (α3) |
GLOGEN |
Type III (α1) |
GLOGEN |
Type XXII (α1) |
GLOGEA |
Type II (α1) |
It is evident that collagen type XXVI does not contain any of these motifs. Thus, in answer to the poster’s question:
Although one cannot exclude that it possesses a hitherto unidentified integrin-binding motif, there is currently no justification for assuming that collagen type XXVI will bind integrin.
Advice to anyone using the RCS Protein Data Bank
Read the documentation on the actual structure file, and the paper in which the structure is reported.