9MYM | pdb_00009mym

Fertilization IZUMO1 Protein Ectodomain

• PDB DOI: https://doi.org/10.2210/pdb9MYM/pdb

• Classification: CELL ADHESION
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-01-22 Released: 2025-03-19 
• Deposition Author(s): Tang, S.
• Funding Organization(s): National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 
  0.191 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Allosteric inhibition of the IZUMO1-JUNO fertilization complex by the naturally occurring antisperm antibody OBF13.

Lu, Y., Ikawa, M., Tang, S.

(2025) Proc Natl Acad Sci U S A 122: e2425952122-e2425952122

• PubMed: 40042902 
• DOI: https://doi.org/10.1073/pnas.2425952122
• Primary Citation of Related Structures:  
  9MYL, 9MYM


• PubMed Abstract: 
  

  Sperm IZUMO1 binds to egg JUNO, and this interaction is essential for mammalian fertilization. Isolated from a female mouse immunized with syngeneic sperm, the antisperm antibody OBF13 recognizes IZUMO1 and inhibits murine fertilization. How OBF13 interferes with sperm-egg interactions was unknown. Here, we present the X-ray crystal structure of IZUMO1 in complex with OBF13. OBF13 binds to the apex of the four-helix domain of IZUMO1, distant from the JUNO-binding site. Our crystal structure of OBF13-bound IZUMO1 resembles apo-IZUMO1 and differs from the structure of IZUMO1 in complex with JUNO. We identify that OBF13 carries a low level of somatic hypermutation, and through deep mutational scanning, we engineer an affinity-enhanced OBF13 variant. This OBF13 variant single-chain fragment variable decreases the apparent affinity of IZUMO1 for membrane-bound murine JUNO and blocks the binding of acrosome-reacted sperm to eggs, thereby preventing fertilization. We propose allostery between the OBF13 epitope and the JUNO-binding site. OBF13 inhibits a conformational change in IZUMO1, preventing fusion-competent sperm from adhering to murine eggs during fertilization. Surprisingly, murine IZUMO1 binds to hamster JUNO with an affinity ~20-fold higher than to murine JUNO. The decreased affinity caused by OBF13 of murine IZUMO1 for hamster JUNO is sufficient for murine sperm to bind to and fuse with hamster eggs. Our studies provide a structural and mechanistic framework for species-specific, allosteric inhibition of IZUMO1 by a naturally occurring antisperm antibody and offer insights into the development of immunocontraceptives.

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Organizational Affiliation: 
• Premium Research Institute for Human Metaverse Medicine, Osaka University, Suita, Osaka 565-0871, Japan.
Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan.
The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.
Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka 565-0871, Japan.
Center for Advanced Modalities and Drug Delivery System, Osaka University, Suita, Osaka 565-0871, Japan.
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 28.37 kDa 
• Atom Count: 2,382 
• Modeled Residue Count: 235 
• Deposited Residue Count: 235 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Izumo sperm-egg fusion protein 1	A	235	Mus musculus	Mutation(s): 0  Gene Names: Izumo1
UniProt
Find proteins for Q9D9J7 (Mus musculus) Explore Q9D9J7  Go to UniProtKB:  Q9D9J7

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	F [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
NAG	B [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
FUC	C [auth A]	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
PEG	E [auth A], G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CA	I [auth A], J [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.191 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.454	α = 90
b = 103.454	β = 90
c = 139.297	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-19 
Deposition Author(s): Tang, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	United States	R00HD104924

Revision History  

• Version 1.0: 2025-03-19
  Type: Initial release