Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A3B1 

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

Macromolecule Content

• Total Structure Weight: 36.40 kDa 
• Atom Count: 2300 
• Residue Count: 314 
• Unique protein chains: 2

2V53

Crystal structure of a SPARC-collagen complex

• DOI: 10.2210/pdb2V53/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2008-10-01 Released: 2008-11-25 
• Deposition Author(s): Hohenester, E., Sasaki, T., Giudici, C., Farndale, R.W., Bachinger, H.P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.320 
• R-Value Work: 0.254 
• R-Value Observed: 0.261 

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 U S A 105: 18273

• PubMed: 19011090 
• DOI: 10.1073/pnas.0808452105
• Structures With Same Primary Citation


• 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 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-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
SPARC	A	230	Homo sapiens	Mutation(s): 0  Gene Names: SPARC, ON
Find proteins for P09486 (Homo sapiens) Explore P09486  Go to UniProtKB:  P09486
NIH Common Fund Data Resources
PHAROS  P09486 GTEx  ENSG00000113140

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
COLLAGEN ALPHA-1(III) CHAIN	B, C, D	33	Homo sapiens	Mutation(s): 0  Gene Names: COL3A1
Find proteins for P02461 (Homo sapiens) Explore P02461  Go to UniProtKB:  P02461
NIH Common Fund Data Resources
PHAROS  P02461 GTEx  ENSG00000168542

Oligosaccharides

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HYP	B,C,D	L-PEPTIDE LINKING	C5 H9 N O3		PRO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.320 
• R-Value Work: 0.254 
• R-Value Observed: 0.261 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.79	α = 90
b = 89.79	β = 90
c = 127.1	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
autoSHARP	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-10-01 
• Released Date: 2008-11-25 
Deposition Author(s): Hohenester, E., Sasaki, T., Giudici, C., Farndale, R.W., Bachinger, H.P.

Revision History 

• Version 1.0: 2008-11-25
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary