+Open data
-Basic information
Entry | Database: PDB / ID: 7ux0 | |||||||||
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Title | Human Sperm TMEM95 Ectodomain | |||||||||
Components | Sperm-egg fusion protein TMEM95 | |||||||||
Keywords | CELL ADHESION / Fertilization / Sperm-egg binding / Sperm-egg fusion / Acrosomal membrane protein | |||||||||
Function / homology | TMEM95 family / TMEM95 family / fusion of sperm to egg plasma membrane involved in single fertilization / acrosomal membrane / sperm plasma membrane / membrane => GO:0016020 / TRIETHYLENE GLYCOL / Sperm-egg fusion protein TMEM95 Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / molecular replacement / Resolution: 1.49 Å | |||||||||
Authors | Tang, S. / Kim, P.S. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: Human sperm TMEM95 binds eggs and facilitates membrane fusion. Authors: Tang, S. / Lu, Y. / Skinner, W.M. / Sanyal, M. / Lishko, P.V. / Ikawa, M. / Kim, P.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ux0.cif.gz | 64.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ux0.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 7ux0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ux0_validation.pdf.gz | 819.5 KB | Display | wwPDB validaton report |
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Full document | 7ux0_full_validation.pdf.gz | 820.9 KB | Display | |
Data in XML | 7ux0_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 7ux0_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/7ux0 ftp://data.pdbj.org/pub/pdb/validation_reports/ux/7ux0 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13805.021 Da / Num. of mol.: 1 / Fragment: ectodomain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TMEM95, UNQ9390/PRO34281 / Production host: Homo sapiens (human) / References: UniProt: Q3KNT9 |
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#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-PGE / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 150 mM NaCl, 20 mM HEPES pH 7.3, 30 mM CaCl2, 2% (w/v) PPG-P400, and 22% (w/v) PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2021 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→36.01 Å / Num. obs: 20505 / % possible obs: 99.7 % / Redundancy: 12.6 % / CC1/2: 0.997 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.49→1.52 Å / Num. unique obs: 1004 / CC1/2: 0.855 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.49→36.01 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.92 Å2 / Biso mean: 30.2975 Å2 / Biso min: 11.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.49→36.01 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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