1H8P

Bull seminal plasma PDC-109 fibronectin type II module


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 
    0.230 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PCClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Sperm Coating Mechanism from the 1.8 A Crystal Structure of Pdc-109-Phosphorylcholine Complex

Wah, D.A.Fernandez-Tornero, C.Sanz, L.Romero, A.Calvete, J.J.

(2002) Structure 10: 505

  • DOI: https://doi.org/10.1016/s0969-2126(02)00751-7
  • Primary Citation of Related Structures:  
    1H8P

  • PubMed Abstract: 

    Bovine seminal plasma PDC-109 binds to sperm surface choline lipids and promotes sperm capacitation by stimulating the efflux of cholesterol and phospholipids. The structure of PDC-109 with bound phosphorylcholine was solved using MAD data of a single platinum site. Its two globular (40 x 50 x 20 A(3)) Fn2 domains are linked and clustered by a short polypeptide. The choline binding sites lie at the same face of the molecule. Phosphorylcholine binds to the Fn2 domains through a cation-pi interaction between the quaternary ammonium group and a core tryptophan, plus hydrogen bonding between hydroxyls of exposed tyrosines and the phosphate group. The structure of the PDC-109-oPC complex provides a structural ground for the sperm membrane-coating mechanism underlying PDC-109-induced capacitation.


  • Organizational Affiliation

    Centro de Investigaciones Biológicas, CSIC, Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SEMINAL PLASMA PROTEIN PDC-109
A, B
109Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P02784 (Bos taurus)
Explore P02784 
Go to UniProtKB:  P02784
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02784
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free:  0.230 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.881α = 90
b = 90.881β = 90
c = 52.21γ = 120
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PCClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-04-12
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection
  • Version 1.4: 2024-11-06
    Changes: Data collection, Database references, Other, Structure summary