1NUB

HELIX C DELETION MUTANT OF BM-40 FS-EC DOMAIN PAIR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.255 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure and mapping by site-directed mutagenesis of the collagen-binding epitope of an activated form of BM-40/SPARC/osteonectin.

Sasaki, T.Hohenester, E.Gohring, W.Timpl, R.

(1998) EMBO J. 17: 1625-1634

  • DOI: 10.1093/emboj/17.6.1625
  • Also Cited By: 2V53

  • PubMed Abstract: 
  • The extracellular calcium-binding domain (positions 138-286) of the matrix protein BM-40 possesses a binding epitope of moderate affinity for several collagen types. This epitope was predicted to reside in helix alphaA and to be partially masked by h ...

    The extracellular calcium-binding domain (positions 138-286) of the matrix protein BM-40 possesses a binding epitope of moderate affinity for several collagen types. This epitope was predicted to reside in helix alphaA and to be partially masked by helix alphaC. Here we show that deletion of helix alphaC produces a 10-fold increase in collagen affinity similar to that seen after proteolytic cleavage of this helix. The predicted removal of the steric constraint was clearly demonstrated by the crystal structure of the mutant at 2.8 A resolution. This constitutively activated mutant was used to map the collagen-binding site following alanine mutagenesis at 13 positions. Five residues were crucial for binding, R149 and N156 in helix alphaA, and L242, M245 and E246 in a loop region connecting the two EF hands of BM-40. These residues are spatially close and form a flat ring of 15 A diameter which matches the diameter of a triple-helical collagen domain. The mutations showed similar effects on binding to collagens I and IV, indicating nearly identical binding sites on both collagens. Selected mutations in the non-activated mutant DeltaI also reduced collagen binding, consistent with the same location of the epitope but in a more cryptic form in intact BM-40.


    Related Citations: 
    • Crystal Structure of a Pair of Follistatin-Like and EF-Hand Calcium-Binding Domains in Bm-40
      Hohenester, E.,Maurer, P.,Timpl, R.
      (1997) Embo J. 16: 3778
    • The Biology of Sparc, a Protein that Modulates Cell-Matrix Interactions
      Lane, T.F.,Sage, E.H.
      (1994) Faseb J. 8: 163


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, D-82152, Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BASEMENT MEMBRANE PROTEIN BM-40
A, B
229Homo sapiensGene Names: SPARC (ON)
Find proteins for P09486 (Homo sapiens)
Go to Gene View: SPARC
Go to UniProtKB:  P09486
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.255 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.860α = 90.00
b = 88.140β = 90.00
c = 153.730γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
X-PLORphasing
X-PLORrefinement
SCALAdata scaling
MOSFLMdata reduction
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-12-30
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance