Database accession: MF5110001
Name: Assembly domain of cartilage oligomeric matrix protein (rat)
PDB ID: 1fbm
Experimental method: X-ray (2.70 Å)
Assembly: homopentamer
Source organism: Rattus norvegicus
Primer publication of the structure:
Guo Y, Bozic D, Malashkevich VN, Kammerer RA, Schulthess T, Engel J
All-trans retinol, vitamin D and other hydrophobic compounds bind in the axial pore of the five-stranded coiled-coil domain of cartilage oligomeric matrix protein.
(1998) EMBO J. 17: 5265-72
PMID: 9736606
Abstract:
The potential storage and delivery function of cartilage oligomeric matrix protein (COMP) for cell signaling molecules was explored by binding hydrophobic compounds to the recombinant five-stranded coiled-coil domain of COMP. Complex formation with benzene, cyclohexane, vitamin D3 and elaidic acid was demonstrated through increases in denaturation temperatures of 2-10 degreesC. For all-trans retinol and all-trans retinoic acid, an equilibrium dissociation constant KD = 0.6 microM was evaluated by fluorescence titration. Binding of benzene and all-trans retinol into the hydrophobic axial pore of the COMP coiled-coil domain was proven by the X-ray crystal structures of the corresponding complexes at 0.25 and 0.27 nm resolution, respectively. Benzene binds with its plane perpendicular to the pore axis. The binding site is between the two internal rings formed by Leu37 and Thr40 pointing into the pore of the COMP coiled-coil domain. The retinol beta-ionone ring is positioned in a hydrophobic environment near Thr40, and the 1.1 nm long isoprene tail follows a completely hydrophobic region of the pore. Its terminal hydroxyl group complexes with a ring of the five side chains of Gln54. A mutant in which Gln54 is replaced by Ile binds all-trans retinol with affinity similar to the wild-type, demonstrating that hydrophobic interactions are predominant.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
calcium ion binding Interacting selectively and non-covalently with calcium ions (Ca2+).
extracellular matrix structural constituent The action of a molecule that contributes to the structural integrity of the extracellular matrix.
Biological process:
extracellular matrix organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
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: 5 distinct polypeptide molecules
Chains: A, B, C, D, E
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 oligomeric matrix protein
Source organism: Rattus norvegicus
Length: 46 residues
Sequence:Sequence according to PDB SEQRESMDLAPQMLRELQETNAALQDVRELLRQQVKEITFLKNTVMECDACG
UniProtKB AC: P35444 (positions: 27-72) Coverage: 6.1%
UniRef90 AC: UniRef90_P49747 (positions: 29-73)
Name: Cartilage oligomeric matrix protein
Source organism: Rattus norvegicus
Length: 46 residues
Sequence:Sequence according to PDB SEQRESMDLAPQMLRELQETNAALQDVRELLRQQVKEITFLKNTVMECDACG
UniProtKB AC: P35444 (positions: 27-72) Coverage: 6.1%
UniRef90 AC: UniRef90_P49747 (positions: 29-73)
Name: Cartilage oligomeric matrix protein
Source organism: Rattus norvegicus
Length: 46 residues
Sequence:Sequence according to PDB SEQRESMDLAPQMLRELQETNAALQDVRELLRQQVKEITFLKNTVMECDACG
UniProtKB AC: P35444 (positions: 27-72) Coverage: 6.1%
UniRef90 AC: UniRef90_P49747 (positions: 29-73)
Name: Cartilage oligomeric matrix protein
Source organism: Rattus norvegicus
Length: 46 residues
Sequence:Sequence according to PDB SEQRESMDLAPQMLRELQETNAALQDVRELLRQQVKEITFLKNTVMECDACG
UniProtKB AC: P35444 (positions: 27-72) Coverage: 6.1%
UniRef90 AC: UniRef90_P49747 (positions: 29-73)
Name: Cartilage oligomeric matrix protein
Source organism: Rattus norvegicus
Length: 46 residues
Sequence:Sequence according to PDB SEQRESMDLAPQMLRELQETNAALQDVRELLRQQVKEITFLKNTVMECDACG
UniProtKB AC: P35444 (positions: 27-72) Coverage: 6.1%
UniRef90 AC: UniRef90_P49747 (positions: 29-73)
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: 9736606). 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). 