5JK9 | pdb_00005jk9

Crystal structure of human IZUMO1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.231 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.194 (Depositor) 
  • R-Value Observed: 
    0.196 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structure of IZUMO1-JUNO reveals sperm-oocyte recognition during mammalian fertilization

Ohto, U.Ishida, H.Krayukhina, E.Uchiyama, S.Inoue, N.Shimizu, T.

(2016) Nature 534: 566-569

  • DOI: https://doi.org/10.1038/nature18596
  • Primary Citation Related Structures: 
    5JK9, 5JKA, 5JKB, 5JKC, 5JKD, 5JKE

  • PubMed Abstract: 

    Fertilization is a fundamental process in sexual reproduction, creating a new individual through the combination of male and female gametes. The IZUMO1 sperm membrane protein and its counterpart oocyte receptor JUNO have been identified as essential factors for sperm-oocyte interaction and fusion. However, the mechanism underlying their specific recognition remains poorly defined. Here, we show the crystal structures of human IZUMO1, JUNO and the IZUMO1-JUNO complex, establishing the structural basis for the IZUMO1-JUNO-mediated sperm-oocyte interaction. IZUMO1 exhibits an elongated rod-shaped structure comprised of a helical bundle IZUMO domain and an immunoglobulin-like domain that are each firmly anchored to an intervening β-hairpin region through conserved disulfide bonds. The central β-hairpin region of IZUMO1 provides the main platform for JUNO binding, while the surface located behind the putative JUNO ligand binding pocket is involved in IZUMO1 binding. Structure-based mutagenesis analysis confirms the biological importance of the IZUMO1-JUNO interaction. This structure provides a major step towards elucidating an essential phase of fertilization and it will contribute to the development of new therapeutic interventions for fertility, such as contraceptive agents.


  • Organizational Affiliation
    • Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

Macromolecule Content 

  • Total Structure Weight: 170.31 kDa 
  • Atom Count: 11,717 
  • Modeled Residue Count: 1,390 
  • Deposited Residue Count: 1,476 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Izumo sperm-egg fusion protein 1
A, B, C, D, E
A, B, C, D, E, F
246Homo sapiensMutation(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
GTEx:  ENSG00000182264 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IYV9
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q8IYV9-1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.231 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.194 (Depositor) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.936α = 77.65
b = 75.067β = 79.11
c = 108.885γ = 70.66
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
autoSHARPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-22
    Type: Initial release
  • Version 1.1: 2016-06-29
    Changes: Database references
  • Version 1.2: 2020-02-19
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2024-11-13
    Changes: Data collection, Database references, Structure summary