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 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

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Ligand Structure Quality Assessment 


This is version 1.3 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: 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 ...

    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.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Diffraction Analysis of Bovine Seminal Plasma Pdc-109, a Protein Composed of Two Fibronectin Type II Domains
      Romero, A., Varela, P.F., Topfer-Petersen, E., Calvete, J.J.
      (1997) Proteins 28: 454

    Organizational Affiliation

    Centro de Investigaciones Biológicas, CSIC, Madrid, Spain.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SEMINAL PLASMA PROTEIN PDC-109A, B109Bos 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PC
Query on PC

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth B],
F [auth B]
PHOSPHOCHOLINE
C5 H15 N O4 P
YHHSONZFOIEMCP-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • 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

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Ligand Structure Quality Assessment 



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