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- PDB-5m5t: Clathrin heavy chain N-terminal domain bound to a non-natural cla... -
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Open data
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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) | ||||||||||||
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![]() | ENDOCYTOSIS | ||||||||||||
Function / homology | ![]() 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 / clathrin coat of coated pit / extrinsic component of synaptic vesicle membrane / Cargo recognition for clathrin-mediated endocytosis / clathrin coat disassembly / clathrin coat assembly / clathrin-coated endocytic vesicle / Clathrin-mediated endocytosis / photoreceptor ribbon synapse / 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 / terminal bouton / phospholipid binding / autophagy / spindle / disordered domain specific binding / melanosome / synaptic vesicle / presynapse / mitotic cell cycle / cytoskeleton / protein domain specific binding / cell division / glutamatergic synapse / synapse / protein-containing complex binding / structural molecule activity / mitochondrion / extracellular exosome / identical protein binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Muenzner, J. / Graham, S.C. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 321.6 KB | Display | ![]() |
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PDB format | ![]() | 261.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 491.5 KB | Display | ![]() |
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Full document | ![]() | 496.9 KB | Display | |
Data in XML | ![]() | 39.2 KB | Display | |
Data in CIF | ![]() | 61.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5m5rC ![]() 5m5sC ![]() 5m5uC ![]() 5m5vC ![]() 5m61C ![]() 1c9iS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 1207.327 Da / Num. of mol.: 6 / Fragment: UNP residues 349-358 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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