1H8P | pdb_00001h8p

Bull seminal plasma PDC-109 fibronectin type II module

• PDB DOI: https://doi.org/10.2210/pdb1H8P/pdb

• Classification: PHOSPHORYLCHOLINE-BINDING PROTEIN
• Organism(s): Bos taurus
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• 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 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

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 
• DOI: https://doi.org/10.1016/s0969-2126(02)00751-7
• Primary Citation 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.

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Organizational Affiliation: 
• Centro de Investigaciones Biológicas, CSIC, Madrid, Spain.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 26.36 kDa 
• Atom Count: 1,737 
• Modeled Residue Count: 176 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PC	C [auth A], D [auth A], E [auth B], F [auth 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 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.881	α = 90
b = 90.881	β = 90
c = 52.21	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  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