+Open data
-Basic information
Entry | Database: PDB / ID: 5jkd | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human IZUMO1-JUNO complex (crystal form 2) | ||||||
Components |
| ||||||
Keywords | CELL ADHESION / fertilization / IZUMO1 / JUNO | ||||||
Function / homology | Function and homology information Acrosome Reaction and Sperm:Oocyte Membrane Binding / protein complex involved in cell-cell adhesion / sperm-egg recognition / protein binding involved in heterotypic cell-cell adhesion / fusion of sperm to egg plasma membrane involved in single fertilization / acrosomal membrane / Post-translational modification: synthesis of GPI-anchored proteins / heterotypic cell-cell adhesion / microvillus membrane / single fertilization ...Acrosome Reaction and Sperm:Oocyte Membrane Binding / protein complex involved in cell-cell adhesion / sperm-egg recognition / protein binding involved in heterotypic cell-cell adhesion / fusion of sperm to egg plasma membrane involved in single fertilization / acrosomal membrane / Post-translational modification: synthesis of GPI-anchored proteins / heterotypic cell-cell adhesion / microvillus membrane / single fertilization / acrosomal vesicle / signaling receptor activity / cell adhesion / external side of plasma membrane / signaling receptor binding / endoplasmic reticulum membrane / protein homodimerization activity / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Ohto, U. / Ishida, H. / Shimizu, T. | ||||||
Citation | Journal: Nature / Year: 2016 Title: Structure of IZUMO1-JUNO reveals sperm-oocyte recognition during mammalian fertilization Authors: Ohto, U. / Ishida, H. / Krayukhina, E. / Uchiyama, S. / Inoue, N. / Shimizu, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5jkd.cif.gz | 193.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5jkd.ent.gz | 152.8 KB | Display | PDB format |
PDBx/mmJSON format | 5jkd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jkd_validation.pdf.gz | 463.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5jkd_full_validation.pdf.gz | 467.6 KB | Display | |
Data in XML | 5jkd_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 5jkd_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/5jkd ftp://data.pdbj.org/pub/pdb/validation_reports/jk/5jkd | HTTPS FTP |
-Related structure data
Related structure data | 5jk9SC 5jkaSC 5jkbC 5jkcC 5jkeC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28163.326 Da / Num. of mol.: 1 / Fragment: UNP residues 22-255 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IZUMO1 / Production host: Drosophila (fruit flies) / References: UniProt: Q8IYV9 | ||||
---|---|---|---|---|---|
#2: Protein | Mass: 25428.842 Da / Num. of mol.: 1 / Fragment: UNP residues 20-228 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IZUMO1R, FOLR4, JUNO / Production host: Drosophila (fruit flies) / References: UniProt: A6ND01 | ||||
#3: Sugar | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.98 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.0 M (NH4)2SO4, 1.0 M KCl, 0.1 M HEPES-NaOH pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 15805 / % possible obs: 99.9 % / Redundancy: 6.6 % / Net I/σ(I): 21.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JK9, 5JKA Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.919 / SU B: 37.844 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R: 1.243 / ESU R Free: 0.358 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 88.915 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.9→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|