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Yorodumi- PDB-5ejn: Crystal structure of Juno, the mammalian egg receptor for sperm Izumo1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ejn | |||||||||||||||||||||
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Title | Crystal structure of Juno, the mammalian egg receptor for sperm Izumo1 | |||||||||||||||||||||
Components | Sperm-egg fusion protein Juno | |||||||||||||||||||||
Keywords | CELL ADHESION / Fertilization / sperm receptor / gamete adhesion / egg-sperm membrane fusion | |||||||||||||||||||||
Function / homology | Function and homology information Post-translational modification: synthesis of GPI-anchored proteins / sperm-egg recognition / fusion of sperm to egg plasma membrane involved in single fertilization / single fertilization / signaling receptor activity / cell adhesion / signaling receptor binding / membrane / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Mus musculus (house mouse) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.703 Å | |||||||||||||||||||||
Authors | Nishimura, K. / Han, L. / Jovine, L. | |||||||||||||||||||||
Funding support | Sweden, 6items
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Citation | Journal: Curr.Biol. / Year: 2016 Title: Divergent evolution of vitamin B9 binding underlies Juno-mediated adhesion of mammalian gametes. Authors: Han, L. / Nishimura, K. / Sadat Al Hosseini, H. / Bianchi, E. / Wright, G.J. / Jovine, L. #1: Journal: Nature / Year: 2014 Title: Juno is the egg Izumo receptor and is essential for mammalian fertilization. Authors: Bianchi, E. / Doe, B. / Goulding, D. / Wright, G.J. #2: Journal: Philos. Trans. R. Soc. Lond., B, Biol. Sci. / Year: 2015 Title: Cross-species fertilization: the hamster egg receptor, Juno, binds the human sperm ligand, Izumo1. Authors: Bianchi, E. / Wright, G.J. #3: Journal: Nature / Year: 2013 Title: Structural basis for molecular recognition of folic acid by folate receptors. Authors: Chen, C. / Ke, J. / Zhou, X.E. / Yi, W. / Brunzelle, J.S. / Li, J. / Yong, E.L. / Xu, H.E. / Melcher, K. #4: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2013 Title: Structures of human folate receptors reveal biological trafficking states and diversity in folate and antifolate recognition. Authors: Wibowo, A.S. / Singh, M. / Reeder, K.M. / Carter, J.J. / Kovach, A.R. / Meng, W. / Ratnam, M. / Zhang, F. / Dann, C.E. #5: Journal: Cell / Year: 2009 Title: Structure of N-terminal domain of NPC1 reveals distinct subdomains for binding and transfer of cholesterol. Authors: Kwon, H.J. / Abi-Mosleh, L. / Wang, M.L. / Deisenhofer, J. / Goldstein, J.L. / Brown, M.S. / Infante, R.E. #6: Journal: EMBO J. / Year: 1997 Title: Crystal structure of chicken riboflavin-binding protein. Authors: Monaco, H.L. | |||||||||||||||||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ejn.cif.gz | 215.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ejn.ent.gz | 175.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ejn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ejn_validation.pdf.gz | 460 KB | Display | wwPDB validaton report |
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Full document | 5ejn_full_validation.pdf.gz | 463.1 KB | Display | |
Data in XML | 5ejn_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 5ejn_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/5ejn ftp://data.pdbj.org/pub/pdb/validation_reports/ej/5ejn | HTTPS FTP |
-Related structure data
Related structure data | 4lrhS 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: 25217.330 Da / Num. of mol.: 2 / Fragment: UNP residues 19-221 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Izumo1r, Folbp3, Folr4, Juno / Plasmid: pHLsec3H / Cell line (production host): HEK-293T / Production host: Homo sapiens (human) / References: UniProt: Q9EQF4 #2: Sugar | ChemComp-NAG / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.72 Å3/Da / Density % sol: 28.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 25% PEG 4000, 0.1 M Tris-HCl pH 8.5, 0.2 M calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection twin | Operator: h,-k,-l / Fraction: 0.49 |
Reflection | Resolution: 2.7→44.83 Å / Num. obs: 9510 / % possible obs: 99.3 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 1.9 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LRH Resolution: 2.703→44.829 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.25 / Stereochemistry target values: TWIN_LSQ_F
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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: 2.703→44.829 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | S33: -0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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