3BN6 | pdb_00003bn6

Crystal Structure of the C2 Domain of Bovine Lactadherin at 1.67 Angstrom Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 
    0.224 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.189 (DCC) 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history

Literature

Crystal structure of lactadherin C2 domain at 1.7A resolution with mutational and computational analyses of its membrane-binding motif.

Shao, C.Novakovic, V.A.Head, J.F.Seaton, B.A.Gilbert, G.E.

(2008) J Biological Chem 283: 7230-7241

  • DOI: https://doi.org/10.1074/jbc.M705195200
  • Primary Citation Related Structures: 
    3BN6

  • PubMed Abstract: 

    Lactadherin is a phosphatidyl-L-serine (Ptd-L-Ser)-binding protein that decorates membranes of milk fat globules. The major Ptd-l-Ser binding function of lactadherin has been localized to its C2 domain, which shares homology with the C2 domains of blood coagulation factor VIII and factor V. Correlating with this homology, purified lactadherin competes efficiently with factors VIII and V for Ptd-L-Ser binding sites, functioning as a potent anticoagulant. We have determined the crystal structure of the lactadherin C2 domain (Lact-C2) at 1.7A resolution. The bovine Lact-C2 structure has a beta-barrel core that is homologous with the factor VIII C2 (fVIII-C2) and factor V C2 (fV-C2) domains. Two loops at the end of the beta-barrel, designated spikes 1 and 3, display four water-exposed hydrophobic amino acids, reminiscent of the membrane-interactive residues of fVIII-C2 and fV-C2. In contrast to the corresponding loops in fVIII-C2 and fV-C2, spike 1 of Lact-C2 adopts a hairpin turn in which the 7-residue loop is stabilized by internal hydrogen bonds. Further, central glycine residues in two membrane-interactive loops may enhance conformability of Lact-C2 to membrane binding sites. Mutagenesis studies confirmed a membrane-interactive role for the hydrophobic and/or Gly residues of both spike 1 and spike 3. Substitution of spike 1 of fVIII-C2 into Lact-C2 also diminished binding. Computational ligand docking studies identified two prospective Ptd-l-Ser interaction sites. These results identify two membrane-interactive loops of Lact-C2 and provide a structural basis for the more efficient phospholipid binding of lactadherin as compared with factor VIII and factor V.


  • Organizational Affiliation
    • Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 02118, USA.

Macromolecule Content 

  • Total Structure Weight: 18 kDa 
  • Atom Count: 1,507 
  • Modeled Residue Count: 158 
  • Deposited Residue Count: 158 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lactadherin158Bos taurusMutation(s): 0 
Gene Names: MFGE8
Membrane Entity: Yes 
UniProt
Find proteins for Q95114 (Bos taurus)
Explore Q95114 
Go to UniProtKB:  Q95114
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ95114
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free:  0.224 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.189 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.909α = 90
b = 56.033β = 90
c = 79.67γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2023-05-31
    Changes: Database references
  • Version 1.4: 2023-09-20
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-11-13
    Changes: Structure summary