Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 26359.31 
• Atom Count: 1532 
• Residue Count: 218 
• Unique protein chains: 1

1H8P

Bull seminal plasma PDC-109 fibronectin type II module

• DOI: 10.2210/pdb1H8P/pdb

• Classification: PHOSPHORYLCHOLINE-BINDING PROTEIN
• Organism(s): Bos taurus


• Deposited: 2001-02-14 Released: 2002-04-12 
• Deposition Author(s): Wah, D.A., Fernandez-Tornero, C., Calvete, J.J., Romero, A.

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Experimental Data Snapshot

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

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

• PubMed: 11937055 


• 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.

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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: Struct.,Funct., Genet. 28: 454




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Organizational Affiliation: 

Centro de Investigaciones Biológicas, CSIC, Madrid, Spain.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
SEMINAL PLASMA PROTEIN PDC-109	A, B	109	Bos taurus	Mutation(s): 0
Find proteins for P02784 (Bos taurus) Go to UniProtKB:  P02784

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PC	A, B	PHOSPHOCHOLINE C5 H15 N O4 P YHHSONZFOIEMCP-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.230 
• R-Value Work: 0.207 
• Space Group: P 3 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 90.881	α = 90.00
b = 90.881	β = 90.00
c = 52.210	γ = 120.00

Software Package:

Software Name	Purpose
CNS	phasing
MOSFLM	data reduction
SCALA	data scaling
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-02-14 
• Released Date: 2002-04-12 
• Deposition Author(s): Wah, D.A., Fernandez-Tornero, C., Calvete, J.J., Romero, A.

Revision History 

• Version 1.0: 2002-04-12
  Type: Initial release
• Version 1.1: 2011-05-07
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2019-07-24
  Type: Data collection