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Yorodumi- PDB-5m5t: Clathrin heavy chain N-terminal domain bound to a non-natural cla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m5t | ||||||||||||
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Title | Clathrin heavy chain N-terminal domain bound to a non-natural clathrin-box motif peptide (Amph4T1) | ||||||||||||
Components |
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Keywords | ENDOCYTOSIS | ||||||||||||
Function / homology | Function and homology information presynaptic endocytic zone / 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 ...presynaptic endocytic zone / 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 / extrinsic component of synaptic vesicle membrane / clathrin coat of coated pit / Cargo recognition for clathrin-mediated endocytosis / clathrin coat disassembly / clathrin coat assembly / photoreceptor ribbon synapse / clathrin-coated endocytic vesicle / Clathrin-mediated endocytosis / leading edge membrane / membrane coat / Clathrin-mediated endocytosis / arrestin family protein binding / positive regulation of endocytosis / synaptic vesicle endocytosis / phosphatase binding / axon terminus / receptor-mediated endocytosis / learning / intracellular protein transport / phospholipid binding / terminal bouton / spindle / autophagy / disordered domain specific binding / melanosome / synaptic vesicle / presynapse / mitotic cell cycle / cytoskeleton / cell division / protein domain specific binding / synapse / glutamatergic synapse / protein-containing complex binding / structural molecule activity / mitochondrion / identical protein binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Bos taurus (cattle) Rattus norvegicus (Norway rat) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||||||||
Authors | Muenzner, J. / Graham, S.C. | ||||||||||||
Funding support | United Kingdom, United States, 3items
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Citation | Journal: Traffic / Year: 2017 Title: Cellular and viral peptides bind multiple sites on the N-terminal domain of clathrin. Authors: Muenzner, J. / Traub, L.M. / Kelly, B.T. / Graham, S.C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m5t.cif.gz | 321.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m5t.ent.gz | 261.2 KB | Display | PDB format |
PDBx/mmJSON format | 5m5t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/5m5t ftp://data.pdbj.org/pub/pdb/validation_reports/m5/5m5t | HTTPS FTP |
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-Related structure data
Related structure data | 5m5rC 5m5sC 5m5uC 5m5vC 5m61C 1c9iS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 40540.473 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal residues 'GS' are residual following cleavage of the purification tag Source: (gene. exp.) Bos taurus (cattle) / Gene: CLTC / Plasmid: pOPT3G / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P49951 #2: Protein/peptide | Mass: 1207.327 Da / Num. of mol.: 6 / Fragment: UNP residues 349-358 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: O08838 #3: Chemical | ChemComp-GOL / | #4: 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 grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1 uL protein:peptide mix (14 mg/mL NTD and 3.4 mM peptide) plus 1 uL reservoir equilibrated against a 200 uL reservoir of 1.1 M sodium malonate pH 8.0 |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91742 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 24, 2015 / Details: toroidal mirrors |
Radiation | Monochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91742 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→33.6 Å / Num. obs: 128743 / % possible obs: 98.2 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.564 / % possible all: 94.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1C9I Resolution: 1.7→33.59 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.358 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.076 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.305 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→33.59 Å
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Refine LS restraints |
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