+Open data
-Basic information
Entry | Database: PDB / ID: 1h0a | ||||||
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Title | Epsin ENTH bound to Ins(1,4,5)P3 | ||||||
Components | EPSIN | ||||||
Keywords | ENDOCYTOSIS / EPSIN / ENTH / CLATHRIN / TRISKELION / COATED VESICLES / ALPHA-ALPHA SUPERHELIX / INS(1 / 4 / 5)P3 | ||||||
Function / homology | Function and homology information positive regulation of clathrin coat assembly / EGFR downregulation / negative regulation of sprouting angiogenesis / clathrin vesicle coat / clathrin coat assembly / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / membrane fission / molecular sequestering activity ...positive regulation of clathrin coat assembly / EGFR downregulation / negative regulation of sprouting angiogenesis / clathrin vesicle coat / clathrin coat assembly / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / membrane fission / molecular sequestering activity / clathrin binding / embryonic organ development / clathrin-coated pit / Notch signaling pathway / female pregnancy / Schaffer collateral - CA1 synapse / terminal bouton / phospholipid binding / endocytosis / presynapse / presynaptic membrane / postsynaptic membrane / in utero embryonic development / transmembrane transporter binding / postsynapse / endosome / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Ford, M.G.J. / McMahon, H.T. / Evans, P.R. | ||||||
Citation | Journal: Nature / Year: 2002 Title: Curvature of Clathrin-Coated Pits Driven by Epsin Authors: Ford, M.G.J. / Mills, I. / Peter, B. / Vallis, Y. / Praefcke, G. / Evans, P.R. / Mcmahon, H.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h0a.cif.gz | 53.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h0a.ent.gz | 38.2 KB | Display | PDB format |
PDBx/mmJSON format | 1h0a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h0a_validation.pdf.gz | 852.5 KB | Display | wwPDB validaton report |
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Full document | 1h0a_full_validation.pdf.gz | 855.3 KB | Display | |
Data in XML | 1h0a_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 1h0a_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/1h0a ftp://data.pdbj.org/pub/pdb/validation_reports/h0/1h0a | HTTPS FTP |
-Related structure data
Related structure data | 1eduS 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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Unit cell |
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-Components
#1: Protein | Mass: 18416.010 Da / Num. of mol.: 1 / Fragment: ENTH DOMAIN, RESIDUES 1-158 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PGEX-4T2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODON PLUS / References: UniProt: O88339 | ||||
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#2: Chemical | ChemComp-DIO / #3: Chemical | ChemComp-I3P / | #4: 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: 3.3 Å3/Da / Density % sol: 62.8 % | ||||||||||||||||||||
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Crystal grow | pH: 7.4 / Details: 35-38% DIOXANE, pH 7.40 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 15, 2001 / Details: BENT MIRROR |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→74.54 Å / Num. obs: 24504 / % possible obs: 97.6 % / Observed criterion σ(I): 6 / Redundancy: 5.88 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 5.9798 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 1.33 / % possible all: 88.5 |
Reflection | *PLUS Lowest resolution: 31.87 Å / % possible obs: 98 % / Redundancy: 5.9 % |
Reflection shell | *PLUS Highest resolution: 1.7 Å / % possible obs: 89 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EDU Resolution: 1.7→74.54 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.725 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS CRYSTALLISATION CONDITIONS CONTAINED A 3-FOLD MOLAR EXCESS OF INS(1,4,5)P3 OVER THE EPSIN ENTH
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→74.54 Å
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Refine LS restraints |
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