2V53

Crystal structure of a SPARC-collagen complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.254 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis of Sequence-Specific Collagen Recognition by Sparc.

Hohenester, E.Sasaki, T.Giudici, C.Farndale, R.W.Bachinger, H.P.

(2008) Proc.Natl.Acad.Sci.USA 105: 18273

  • DOI: 10.1073/pnas.0808452105

  • PubMed Abstract: 
  • Protein interactions with the collagen triple helix play a critical role in collagen fibril formation, cell adhesion, and signaling. However, structural insight into sequence-specific collagen recognition is limited to an integrin-peptide complex. A ...

    Protein interactions with the collagen triple helix play a critical role in collagen fibril formation, cell adhesion, and signaling. However, structural insight into sequence-specific collagen recognition is limited to an integrin-peptide complex. A GVMGFO motif in fibrillar collagens (O denotes 4-hydroxyproline) binds 3 unrelated proteins: von Willebrand factor (VWF), discoidin domain receptor 2 (DDR2), and the extracellular matrix protein SPARC/osteonectin/BM-40. We report the crystal structure at 3.2 A resolution of human SPARC bound to a triple-helical 33-residue peptide harboring the promiscuous GVMGFO motif. SPARC recognizes the GVMGFO motifs of the middle and trailing collagen chains, burying a total of 720 A(2) of solvent-accessible collagen surface. SPARC binding does not distort the canonical triple helix of the collagen peptide. In contrast, a critical loop in SPARC is substantially remodelled upon collagen binding, creating a deep pocket that accommodates the phenylalanine residue of the trailing collagen chain ("Phe pocket"). This highly restrictive specificity pocket is shared with the collagen-binding integrin I-domains but differs strikingly from the shallow collagen-binding grooves of the platelet receptor glycoprotein VI and microbial adhesins. We speculate that binding of the GVMGFO motif to VWF and DDR2 also results in structural changes and the formation of a Phe pocket.


    Related Citations: 
    • 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


    Organizational Affiliation

    Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom. e.hohenester@imperial.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SPARC
A
230Homo sapiensGene Names: SPARC (ON)
Find proteins for P09486 (Homo sapiens)
Go to Gene View: SPARC
Go to UniProtKB:  P09486
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
COLLAGEN ALPHA-1(III) CHAIN
B, C, D
33Homo sapiensGene Names: COL3A1
Find proteins for P02461 (Homo sapiens)
Go to Gene View: COL3A1
Go to UniProtKB:  P02461
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

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

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HYP
Query on HYP
B, C, D
L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.254 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 89.790α = 90.00
b = 89.790β = 90.00
c = 127.100γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing
autoSHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-25
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance