+Open data
-Basic information
Entry | Database: PDB / ID: 2qy7 | ||||||
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Title | Crystal structure of human epsinR ENTH domain | ||||||
Components | Clathrin interactor 1 | ||||||
Keywords | PROTEIN BINDING / ENTH domain / epsin / Alternative splicing / Cytoplasm / Cytoplasmic vesicle / Endocytosis / Lipid-binding / Membrane / Phosphorylation | ||||||
Function / homology | Function and homology information clathrin vesicle coat / clathrin coat assembly / clathrin binding / Golgi Associated Vesicle Biogenesis / phospholipid binding / endocytosis / endosome / cadherin binding / intracellular membrane-bounded organelle / perinuclear region of cytoplasm ...clathrin vesicle coat / clathrin coat assembly / clathrin binding / Golgi Associated Vesicle Biogenesis / phospholipid binding / endocytosis / endosome / cadherin binding / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Miller, S.E. / Collins, B.M. / McCoy, A.J. / Robinson, M.S. / Owen, D.J. | ||||||
Citation | Journal: Nature / Year: 2007 Title: A SNARE-adaptor interaction is a new mode of cargo recognition in clathrin-coated vesicles. Authors: Miller, S.E. / Collins, B.M. / McCoy, A.J. / Robinson, M.S. / Owen, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qy7.cif.gz | 100.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qy7.ent.gz | 78.3 KB | Display | PDB format |
PDBx/mmJSON format | 2qy7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/2qy7 ftp://data.pdbj.org/pub/pdb/validation_reports/qy/2qy7 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 17434.732 Da / Num. of mol.: 3 / Fragment: epsinR ENTH domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLINT1, ENTH, EPN4, EPNR, KIAA0171 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q14677 #2: 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: 2.05 Å3/Da / Density % sol: 39.86 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 30% (w/v) PEG3000, 100 mM CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9816 Å |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9816 Å / Relative weight: 1 |
Reflection | Resolution: 2→36.4 Å / Num. obs: 28679 / % possible obs: 99.1 % / Observed criterion σ(F): 3.5 / Redundancy: 4.4 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 3.5 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→36.35 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.902 / SU B: 4.263 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.049 Å2
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Refinement step | Cycle: LAST / Resolution: 2→36.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.995→2.047 Å / Total num. of bins used: 20
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