+Open data
-Basic information
Entry | Database: PDB / ID: 5f4v | ||||||
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Title | Crystal structure of the human sperm Izumo1 residues 22-268 | ||||||
Components | Izumo sperm-egg fusion protein 1 | ||||||
Keywords | CELL ADHESION / glycoprotein / membrane-bound / cysteine-rich / adhesion / fusion | ||||||
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 / heterotypic cell-cell adhesion / single fertilization / acrosomal vesicle / cell adhesion ...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 / heterotypic cell-cell adhesion / single fertilization / acrosomal vesicle / cell adhesion / signaling receptor binding / endoplasmic reticulum membrane / protein homodimerization activity / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Aydin, H. / Sultana, A. / Lee, J.E. | ||||||
Citation | Journal: Nature / Year: 2016 Title: Molecular architecture of the human sperm IZUMO1 and egg JUNO fertilization complex. Authors: Aydin, H. / Sultana, A. / Li, S. / Thavalingam, A. / Lee, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f4v.cif.gz | 107.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f4v.ent.gz | 81.6 KB | Display | PDB format |
PDBx/mmJSON format | 5f4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/5f4v ftp://data.pdbj.org/pub/pdb/validation_reports/f4/5f4v | HTTPS FTP |
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-Related structure data
Related structure data | 5f4eSC 5f4qC 5f4tC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28780.166 Da / Num. of mol.: 1 / Fragment: UNP residues 22-268 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IZUMO1 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q8IYV9 |
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#2: Sugar | ChemComp-NAG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.46 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.085 M HEPES sodium salt (pH 7.5), 8.5% (v/v) isopropanol, 17% (w/v) PEG 4000 and 15% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å | |||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 30, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.9→47.603 Å / Num. obs: 6484 / % possible obs: 100 % / Redundancy: 5.8 % / Biso Wilson estimate: 49.33 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.055 / Net I/σ(I): 12.9 / Num. measured all: 37350 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5F4E Resolution: 2.9→47.603 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 24.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→47.603 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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