+Open data
-Basic information
Entry | Database: PDB / ID: 5jka | |||||||||
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Title | Crystal structure of human JUNO (crystal form 1) | |||||||||
Components | Sperm-egg fusion protein Juno | |||||||||
Keywords | CELL ADHESION / fertilization / IZUMO1 / JUNO | |||||||||
Function / homology | Function and homology information sperm-egg recognition / fusion of sperm to egg plasma membrane involved in single fertilization / Post-translational modification: synthesis of GPI-anchored proteins / microvillus membrane / single fertilization / signaling receptor activity / cell adhesion / external side of plasma membrane / signaling receptor binding / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jka.cif.gz | 182.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jka.ent.gz | 142.5 KB | Display | PDB format |
PDBx/mmJSON format | 5jka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/5jka ftp://data.pdbj.org/pub/pdb/validation_reports/jk/5jka | HTTPS FTP |
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-Related structure data
Related structure data | 5jk9C 5jkbC 5jkcC 5jkdC 5jkeC 4kmyS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25428.842 Da / Num. of mol.: 2 / 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 #2: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG3350, 0.24 M malonate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 22, 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→50 Å / Num. obs: 33749 / % possible obs: 99.2 % / Redundancy: 12.3 % / Net I/σ(I): 26.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KMY Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 8.581 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.146 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.833 Å2
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Refinement step | Cycle: 1 / Resolution: 2→50 Å
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Refine LS restraints |
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