5B5K | pdb_00005b5k

Crystal structure of Izumo1, the mammalian sperm ligand for egg Juno

• PDB DOI: https://doi.org/10.2210/pdb5B5K/pdb

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


• Deposited: 2016-05-11 Released: 2016-07-06 
• Deposition Author(s): Nishimura, K., Han, L., De Sanctis, D., Jovine, L.
• Funding Organization(s): Karolinska Institutet, Swedish Research Council, Goran Gustafsson Foundation for Research in Natural Sciences and Medicine, Sven and Ebba-Christina Hagberg foundation, EMBO Young Investigator, European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.281 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.257 (Depositor), 0.267 (DCC) 
• R-Value Observed: 
  0.258 (Depositor) 

Starting Model: experimental

Literature

The structure of sperm Izumo1 reveals unexpected similarities with Plasmodium invasion proteins.

Nishimura, K., Han, L., Bianchi, E., Wright, G.J., de Sanctis, D., Jovine, L.

(2016) Curr Biol 26: R661-R662

• PubMed: 27374339 
• DOI: https://doi.org/10.1016/j.cub.2016.06.028
• Primary Citation Related Structures: 
  5B5K


• PubMed Abstract: 
  

  Fertilization, the culminating event in sexual reproduction, occurs when haploid sperm and egg recognize each other and fuse to form a diploid zygote. In mammals this process critically depends on the interaction between Izumo1, a protein exposed on the equatorial segment of acrosome-reacted sperm, and the egg plasma-membrane-anchored receptor Juno [1,2]. The molecular mechanism triggering gamete fusion is unresolved because both Izumo1 and Juno lack sequence similarity to known membrane fusogens. Here we report the crystal structure of Izumo1, which reveals a membrane distal region composed of a four-helix bundle connected to a carboxy-terminal immunoglobulin (Ig)-like domain through a β-hairpin stabilized by disulfide bonds. Remarkably, different regions of Izumo1 display significant structural similarities to two proteins expressed by the invasive sporozoite stage of Plasmodium parasites: SPECT1, which is essential for host cell traversal and hepatocyte invasion [3]; and TRAP, which is necessary for gliding motility and invasion [4]. These observations suggest a link between the molecular mechanisms underlying host cell invasion by the malaria parasite and gamete membrane fusion at fertilization.

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Organizational Affiliation: 
• Department of Biosciences and Nutrition & Center for Innovative Medicine, Karolinska Institutet, Huddinge, SE-141 83, Sweden.
Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
ESRF - The European Synchrotron, Grenoble 38000, France.
Department of Biosciences and Nutrition & Center for Innovative Medicine, Karolinska Institutet, Huddinge, SE-141 83, Sweden. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.79 kDa 
• Atom Count: 1,960 
• Modeled Residue Count: 235 
• Deposited Residue Count: 236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Izumo sperm-egg fusion protein 1	A	236	Mus musculus	Mutation(s): 0  Gene Names: Izumo1
UniProt
Find proteins for Q9D9J7 (Mus musculus) Explore Q9D9J7  Go to UniProtKB:  Q9D9J7
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q9D9J7-1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	C [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
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: 2.50 Å
• R-Value Free:  0.281 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.257 (Depositor), 0.267 (DCC) 
• R-Value Observed: 0.258 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.28	α = 90
b = 103.28	β = 90
c = 139.27	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-07-06 
Deposition Author(s): Nishimura, K., Han, L., De Sanctis, D., Jovine, L.

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Funding Organization	Location	Grant Number
Karolinska Institutet	Sweden	--
Swedish Research Council	Sweden	2012-5093
Goran Gustafsson Foundation for Research in Natural Sciences and Medicine	Sweden	--
Sven and Ebba-Christina Hagberg foundation	Sweden	--
EMBO Young Investigator		--
European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)		ERC 260759

Revision History  

• Version 1.0: 2016-07-06
  Type: Initial release
  
• Version 1.1: 2016-08-03
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2024-10-23
  Changes: Structure summary