Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 27.40 kDa 
• Atom Count: 1751 
• Modelled Residue Count: 235 
• Deposited Residue Count: 239 
• Unique protein chains: 1

5F4T

Crystal structure of the human sperm Izumo1 residues 22-254

• PDB DOI: 10.2210/pdb5F4T/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2015-12-03 Released: 2016-06-15 
• Deposition Author(s): Aydin, H., Sultana, A., Lee, J.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.08 Å
• R-Value Free: 0.248 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 

Literature

Molecular architecture of the human sperm IZUMO1 and egg JUNO fertilization complex.

Aydin, H., Sultana, A., Li, S., Thavalingam, A., Lee, J.E.

(2016) Nature 534: 562-565

• PubMed: 27309818 
• DOI: 10.1038/nature18595
• Primary Citation of Related Structures:  
  5F4E, 5F4Q, 5F4T, 5F4V


• PubMed Abstract: 
  

Fertilization is an essential biological process in sexual reproduction and comprises a series of molecular interactions between the sperm and egg. The fusion of the haploid spermatozoon and oocyte is the culminating event in mammalian fertilization, enabling the creation of a new, genetically distinct diploid organism. The merger of two gametes is achieved through a two-step mechanism in which the sperm protein IZUMO1 on the equatorial segment of the acrosome-reacted sperm recognizes its receptor, JUNO, on the egg surface. This recognition is followed by the fusion of the two plasma membranes. IZUMO1 and JUNO proteins are indispensable for fertilization, as constitutive knockdown of either protein results in mice that are healthy but infertile. Despite their central importance in reproductive medicine, the molecular architectures of these proteins and the details of their functional roles in fertilization are not known. Here we present the crystal structures of human IZUMO1 and JUNO in unbound and bound conformations. The human IZUMO1 structure exhibits a distinct boomerang shape and provides structural insights into the IZUMO family of proteins. Human IZUMO1 forms a high-affinity complex with JUNO and undergoes a major conformational change within its N-terminal domain upon binding to the egg-surface receptor. Our results provide insights into the molecular basis of sperm-egg recognition, cross-species fertilization, and the barrier to polyspermy, thereby promising benefits for the rational development of non-hormonal contraceptives and fertility treatments for humans and other mammals.

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Organizational Affiliation: 

Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Izumo sperm-egg fusion protein 1	A	239	Homo sapiens	Mutation(s): 0  Gene Names: IZUMO1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IYV9 (Homo sapiens) Explore Q8IYV9  Go to UniProtKB:  Q8IYV9
PHAROS:  Q8IYV9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.08 Å
• R-Value Free: 0.248 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.039	α = 90
b = 126.039	β = 90
c = 60.895	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-12-03 
• Released Date: 2016-06-15 
Deposition Author(s): Aydin, H., Sultana, A., Lee, J.E.

Revision History  

• Version 1.0: 2016-06-15
  Type: Initial release
  
• Version 1.1: 2016-06-29
  Changes: Database references
• Version 1.2: 2016-07-06
  Changes: Database references
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary