1FBM

ASSEMBLY DOMAIN OF CARTILAGE OLIGOMERIC MATRIX PROTEIN IN COMPLEX WITH ALL-TRANS RETINOL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

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.

Guo, Y.Bozic, D.Malashkevich, V.N.Kammerer, R.A.Schulthess, T.

(1998) EMBO J 17: 5265-5272

  • DOI: 10.1093/emboj/17.18.5265
  • Structures With Same Primary Citation

  • PubMed 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 b ...

    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.


    Related Citations: 
    • Crystallization and Preliminary Crystallographic Study of the Pentamerizing Domain from Cartilage Oligomeric Matrix Protein: a Five-stranded Alpha-helical Bundle.
      Efimov, V.P., Engel, J., Malashkevich, V.N.
      (1996) Proteins 24: 259
    • The Crystal Structure of a Five-stranded Coiled Coil in COMP: a Prototype Ion Channel?
      Malashkevich, V.N., Kammerer, R.A., Efimov, V.P., Schulthess, T., Engel, J.
      (1996) Science 274: 761

    Organizational Affiliation

    Abteilung für Biophysikalische Chemie, Biozentrum, Universität Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (CARTILAGE OLIGOMERIC MATRIX PROTEIN)
A, B, C, D, E
46Rattus norvegicusMutation(s): 0 
Gene Names: Comp
Find proteins for P35444 (Rattus norvegicus)
Go to UniProtKB:  P35444
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RTL
Query on RTL

Download CCD File 
B
RETINOL
C20 H30 O
FPIPGXGPPPQFEQ-OVSJKPMPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RTLKd :  600   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.47α = 90
b = 49.47β = 103.84
c = 54.98γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
ROTAVATAdata reduction
AMoREphasing
X-PLORrefinement
CCP4data scaling
ROTAVATAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-08-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2018-01-31
    Changes: Experimental preparation
  • Version 1.5: 2018-02-28
    Changes: Experimental preparation