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 1.6 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: https://doi.org/10.1093/emboj/17.18.5265
  • Primary Citation of Related Structures:  
    1FBM

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (CARTILAGE OLIGOMERIC MATRIX PROTEIN)
A, B, C, D, E
46Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P35444 (Rattus norvegicus)
Explore P35444 
Go to UniProtKB:  P35444
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35444
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RTL
Query on RTL

Download Ideal Coordinates CCD File 
F [auth B]RETINOL
C20 H30 O
FPIPGXGPPPQFEQ-OVSJKPMPSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
RTL PDBBind:  1FBM Kd: 600 (nM) from 1 assay(s)
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  (Full details and data files)

  • 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
  • Version 1.6: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Structure summary