9H4R | pdb_00009h4r

Structure of fertilization-blocking monoclonal antibody IE-3 VHVL bound to the ZP-N1 domain of mouse ZP2 (crystal form I)

• PDB DOI: https://doi.org/10.2210/pdb9H4R/pdb

• Classification: CELL ADHESION
• Organism(s): Mus musculus, Rattus norvegicus
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2024-10-21 Released: 2025-03-12 
• Deposition Author(s): Dioguardi, E., De Sanctis, D., Jovine, L.
• Funding Organization(s): Swedish Research Council, European Research Council (ERC), Knut and Alice Wallenberg Foundation, European Molecular Biology Organization (EMBO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.233 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Models: experimental

Literature

Structural basis of ZP2-targeted female nonhormonal contraception.

Dioguardi, E., Stsiapanava, A., Fahrenkamp, E., Han, L., de Sanctis, D., Inzunza, J., Jovine, L.

(2025) Proc Natl Acad Sci U S A 122: e2426057122-e2426057122

• PubMed: 40215272 
• DOI: https://doi.org/10.1073/pnas.2426057122
• Primary Citation of Related Structures:  
  9H4R, 9H4S


• PubMed Abstract: 
  

  Monoclonal antibody IE-3 prevents mouse fertilization by binding ZP2, a major component of the oocyte-specific zona pellucida (ZP). We show that an IE-3-derived single-chain variable fragment (scFV) is sufficient for blocking fertilization in vitro and determine the structural basis of IE-3/ZP2 recognition. The high affinity of this interaction depends on induced fit of the epitope, offering insights for nonhormonal contraceptive design without off-target effects.

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Organizational Affiliation: 
• Department of Medicine, Karolinska Institutet, Huddinge 14183, Sweden.
European Synchrotron Radiation Facility-The European Synchrotron, Grenoble 38000, France.
Department of Laboratory Medicine, Karolinska Institutet, Huddinge 14152, Sweden.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 78.26 kDa 
• Atom Count: 5,768 
• Modeled Residue Count: 663 
• Deposited Residue Count: 704 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zona pellucida sperm-binding protein 2	A, D [auth B]	112	Mus musculus	Mutation(s): 1  Gene Names: Zp2, Zp-2, Zpa
UniProt
Find proteins for P20239 (Mus musculus) Explore P20239  Go to UniProtKB:  P20239

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain variable (VH) domain of anti-ZP2 monoclonal antibody IE-3	B [auth H], E [auth X]	123	Rattus norvegicus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain variable (VL) domain of anti-ZP2 monoclonal antibody IE-3	C [auth L], F [auth Y]	117	Rattus norvegicus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.233 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.64	α = 90
b = 92.29	β = 90
c = 91.17	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Dioguardi, E., De Sanctis, D., Jovine, L.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2012-5093
Swedish Research Council	Sweden	2016-03999
Swedish Research Council	Sweden	2020-04936
European Research Council (ERC)	European Union	ERC 260759
Knut and Alice Wallenberg Foundation	Sweden	2018.0042
European Molecular Biology Organization (EMBO)	European Union	EMBO Young Investigator

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release
  
• Version 1.1: 2025-04-23
  Changes: Database references