Database accession: MF3110001
Name: Assembly domain of cartilage oligomeric matrix protein (chicken)
PDB ID: 1aq5
Experimental method: NMR
Assembly: homotrimer
Source organism: Gallus gallus
Primer publication of the structure:
Dames SA, Kammerer RA, Wiltscheck R, Engel J, Alexandrescu AT
NMR structure of a parallel homotrimeric coiled coil.
(1998) Nat. Struct. Biol. 5: 687-91
PMID: 9699631
Abstract:
The solution structure of the oligomerization domain of cartilage matrix protein (also known as matrilin-1) has been determined by heteronuclear NMR spectroscopy. The domain folds into a parallel, disulfide-linked, three-stranded, alpha-helical coiled coil, spanning five heptad repeats in the amino acid sequence. The sequence of the first two heptad repeats shows some deviations from the consensus of hydrophobic and hydrophilic residue preferences. While the corresponding region of the coiled coil has a higher intrinsic flexibility, backbone alpha-helix and superhelix parameters are consistent with a regular coiled coil structure.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
extracellular matrix structural constituent The action of a molecule that contributes to the structural integrity of the extracellular matrix.
calcium ion binding Interacting selectively and non-covalently with calcium ions (Ca2+).
Biological process: not assigned
Cellular component:
proteinaceous extracellular matrix A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.
Structural annotations of the participating protein chains.Entry contents: 3 distinct polypeptide molecules
Chains: A, B, C
Notes: No modifications of the original PDB file. Chain identifiers are identical with the PDB's identifiers.
Number of unique protein segments: 1
Name: Cartilage matrix protein
Source organism: Gallus gallus
Length: 47 residues
Sequence:Sequence according to PDB SEQRESGSHMEEDPCECKSIVKFQTKVEELINTLQQKLEAVAKRIEALENKII
UniProtKB AC: P05099 (positions: 447-493) Coverage: 9.5%
UniRef90 AC: UniRef90_P05099 (positions: 450-493)
Name: Cartilage matrix protein
Source organism: Gallus gallus
Length: 47 residues
Sequence:Sequence according to PDB SEQRESGSHMEEDPCECKSIVKFQTKVEELINTLQQKLEAVAKRIEALENKII
UniProtKB AC: P05099 (positions: 447-493) Coverage: 9.5%
UniRef90 AC: UniRef90_P05099 (positions: 450-493)
Name: Cartilage matrix protein
Source organism: Gallus gallus
Length: 47 residues
Sequence:Sequence according to PDB SEQRESGSHMEEDPCECKSIVKFQTKVEELINTLQQKLEAVAKRIEALENKII
UniProtKB AC: P05099 (positions: 447-493) Coverage: 9.5%
UniRef90 AC: UniRef90_P05099 (positions: 450-493)
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Complex evidence:
The subunits in the structure are bound via coiled coil interactions (PMID: 9699631). Coiled coils are highly versatile folding units (PMID: 11166216), where the formation of the structure and the interaction between subunits is almost ubiquitously linked. This cooperative nature of binding and folding that results in a two-step process has been demonstrated for coiled coils with varying oligomeric state from dimers (PMID: 9811815) and trimers (PMID: 10933510) up to heptamers (PMID: 17030805). While the interaction and folding are linked, in certain cases there can be significant residual structure before association (PMID: 8401212). However, these residual structural elements usually encompass 1-2 turns of helices that serve as a 'nucleation site' driving interaction and helix formation (zipping up) (PMID: 17438295), thus even in these cases monomeric coiled coil subunits cannot be considered to have a stable structure.
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). No related structure was found in the Protein Data Bank.
