Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26.78 kDa 
• Atom Count: 2003 
• Modelled Residue Count: 230 
• Deposited Residue Count: 230 
• Unique protein chains: 1

1FBM

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

• PDB DOI: 10.2210/pdb1FBM/pdb

• Classification: CELL ADHESION
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2000-07-16 Released: 2000-08-02 
• Deposition Author(s): Guo, Y., Bozic, D., Malashkevich, V.N., Kammerer, R.A., Schulthess, T.

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Experimental Data Snapshot

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

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

• PubMed: 9736606 
• DOI: 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (CARTILAGE OLIGOMERIC MATRIX PROTEIN)	A, B, C, D, E	46	Rattus norvegicus	Mutation(s): 0  Gene Names: Comp
UniProt
Find proteins for P35444 (Rattus norvegicus) Explore P35444  Go to UniProtKB:  P35444

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RTL	F [auth B]	RETINOL C20 H30 O FPIPGXGPPPQFEQ-OVSJKPMPSA-N

Binding Affinity Annotations
ID	Source	Binding 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 = 38.47	α = 90
b = 49.47	β = 103.84
c = 54.98	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
ROTAVATA	data reduction
AMoRE	phasing
X-PLOR	refinement
CCP4	data scaling
ROTAVATA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-07-16 
• Released Date: 2000-08-02 
Deposition Author(s): Guo, Y., Bozic, D., Malashkevich, V.N., Kammerer, R.A., Schulthess, T.

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