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Open data
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Basic information
Entry | Database: PDB / ID: 5jke | ||||||
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Title | Crystal structure of human IZUMO1-JUNO complex (crystal form 3) | ||||||
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![]() | CELL ADHESION / fertilization / IZUMO1 / JUNO | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ohto, U. / Ishida, H. / Shimizu, T. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 364.8 KB | Display | ![]() |
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PDB format | ![]() | 299.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 492.9 KB | Display | ![]() |
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Full document | ![]() | 503.2 KB | Display | |
Data in XML | ![]() | 32.1 KB | Display | |
Data in CIF | ![]() | 43.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jk9SC ![]() 5jkaSC ![]() 5jkbC ![]() 5jkcC ![]() 5jkdC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 28163.326 Da / Num. of mol.: 2 / Fragment: UNP residues 20-255 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: 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.) ![]() ![]() ![]() |
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-Sugars , 1 types, 4 molecules ![](data/chem/img/NAG.gif)
#3: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 8 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG4000, 0.2 M Li2SO4, 0.1 M MES-NaOH pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 2.86→48.3 Å / Num. obs: 31399 / % possible obs: 100 % / Redundancy: 13.2 % / Net I/σ(I): 28.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5JK9, 5JKA Resolution: 2.86→48.3 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 32.653 / SU ML: 0.278 / Cross valid method: THROUGHOUT / ESU R: 1.232 / ESU R Free: 0.337 / 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: 86.849 Å2
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Refinement step | Cycle: 1 / Resolution: 2.86→48.3 Å
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Refine LS restraints |
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