+Open data
-Basic information
Entry | Database: PDB / ID: 1utc | ||||||
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Title | Clathrin terminal domain complexed with TLPWDLWTT | ||||||
Components |
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Keywords | ENDOCYTOSIS / CLATHRIN / CYTOSKELETON | ||||||
Function / homology | Function and homology information Retrograde neurotrophin signalling / Recycling pathway of L1 / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Gap junction degradation / Formation of annular gap junctions / Golgi Associated Vesicle Biogenesis / RHOU GTPase cycle / RHOV GTPase cycle ...Retrograde neurotrophin signalling / Recycling pathway of L1 / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Gap junction degradation / Formation of annular gap junctions / Golgi Associated Vesicle Biogenesis / RHOU GTPase cycle / RHOV GTPase cycle / clathrin coat of trans-Golgi network vesicle / Lysosome Vesicle Biogenesis / clathrin light chain binding / negative regulation of hyaluronan biosynthetic process / clathrin complex / MHC class II antigen presentation / VLDLR internalisation and degradation / clathrin coat of coated pit / Cargo recognition for clathrin-mediated endocytosis / clathrin coat disassembly / clathrin coat assembly / clathrin-coated endocytic vesicle / leading edge membrane / membrane coat / Clathrin-mediated endocytosis / arrestin family protein binding / synaptic vesicle endocytosis / receptor-mediated endocytosis / intracellular protein transport / phospholipid binding / synaptic vesicle membrane / autophagy / spindle / endocytosis / disordered domain specific binding / Clathrin-mediated endocytosis / actin cytoskeleton / melanosome / synaptic vesicle / mitotic cell cycle / chemical synaptic transmission / protein domain specific binding / cell division / structural molecule activity / mitochondrion / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | BOS TAURUS (cattle) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Miele, A.E. / Evans, P.R. / Owen, D.J. | ||||||
Citation | Journal: Nat. Struct. Mol. Biol. / Year: 2004 Title: Two distinct interaction motifs in amphiphysin bind two independent sites on the clathrin terminal domain beta-propeller. Authors: Miele, A.E. / Watson, P.J. / Evans, P.R. / Traub, L.M. / 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 | 1utc.cif.gz | 157 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1utc.ent.gz | 124.5 KB | Display | PDB format |
PDBx/mmJSON format | 1utc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1utc_validation.pdf.gz | 445.2 KB | Display | wwPDB validaton report |
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Full document | 1utc_full_validation.pdf.gz | 455.6 KB | Display | |
Data in XML | 1utc_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 1utc_validation.cif.gz | 44.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/1utc ftp://data.pdbj.org/pub/pdb/validation_reports/ut/1utc | HTTPS FTP |
-Related structure data
Related structure data | 1c9iS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.999979, -0.005338, 0.00362), Vector: Details | CLATHRIN HEAVY CHAIN IS A MONOMER BIOLOGICALLY BUTIS CLASSIFIED AS A DIMER IN THIS ENTRY SINCE EVERYMOLECULE OF CLATHRIN (CHAINS A AND B) ARE BOUND TOA PEPTIDE. | |
-Components
#1: Antibody | Mass: 40396.340 Da / Num. of mol.: 2 / Fragment: TERMINAL DOMAIN, RESIDUES 1-363 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOS TAURUS (cattle) / Plasmid: PGEX4T2 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: P49951 #2: Protein/peptide | Mass: 1132.264 Da / Num. of mol.: 2 / Fragment: W-BOX, RESIDUES 379-387 / Source method: obtained synthetically / Details: PEPTIDE FROM AMPHIPHYSIN 1 / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P49418 #3: Water | ChemComp-HOH / | Compound details | CLATHRIN IS THE MAJOR PROTEIN OF THE POLYHEDRAL COAT OF COATED PITS & VESICLES. TWO DIFFERENT ...CLATHRIN IS THE MAJOR PROTEIN OF THE POLYHEDRAL | |
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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: 2.38 Å3/Da / Density % sol: 48.28 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 9 Details: VAPOUR DIFFUSION OVER A RESERVOIR CONTAINING 20% PEG8000, 200 MM MGCL2, 4 MM DTT,100 MM CAPS PH 9, DRIED UP DROP | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 9 / Method: vapor diffusion, hanging 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: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→24.92 Å / Num. obs: 37228 / % possible obs: 99.4 % / Redundancy: 5.84 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 9.3131 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 4.33 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.02 / % possible all: 97.4 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 29.9 Å / Num. obs: 37078 / Redundancy: 5.8 % / Num. measured all: 495661 / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS % possible obs: 97.2 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 5.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1C9I Resolution: 2.3→105.41 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.892 / SU B: 7.03 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.245 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.21 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→105.41 Å
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Refine LS restraints |
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