5F4V Cell Adhesion date Dec 03, 2015
title Crystal Structure Of The Human Sperm Izumo1 Residues 22-268
authors H.Aydin, A.Sultana, J.E.Lee
compound source
Molecule: Izumo Sperm-Egg Fusion Protein 1
Chain: A
Fragment: Unp Residues 22-268
Synonym: Oocyte Bindingfusion Factor,Obf,Sperm-Specific Pr Izumo;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Izumo1
Expression_system: Drosophila Melanogaster
Expression_system_common: Fruit Fly
Expression_system_taxid: 7227
symmetry Space Group: H 3
R_factor 0.188 R_Free 0.232
length a length b length c angle alpha angle beta angle gamma
121.300 121.300 53.400 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.90 Å
ligand NAG enzyme

Primary referenceMolecular architecture of the human sperm IZUMO1 and egg JUNO fertilization complex., Aydin H, Sultana A, Li S, Thavalingam A, Lee JE, Nature. 2016 Jun 15;534(7608):562-5. doi: 10.1038/nature18595. PMID:27309818
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (81 Kb) [Save to disk]
  • Biological Unit Coordinates (5f4v.pdb1.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 5F4V
  • CSU: Contacts of Structural Units for 5F4V
  • Structure Factors (444 Kb)
  • Retrieve 5F4V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5F4V from S2C, [Save to disk]
  • Re-refined 5f4v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5F4V in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5F4V
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5f4v from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5f4v] [5f4v_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5F4V: [IG ] by SMART
  • Other resources with information on 5F4V
  • Community annotation for 5F4V at PDBWiki (http://pdbwiki.org)

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