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- PDB-5m5s: Clathrin heavy chain N-terminal domain bound to amphiphysin clath... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5m5s | ||||||||||||
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Title | Clathrin heavy chain N-terminal domain bound to amphiphysin clathrin-box motif | ||||||||||||
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![]() | ENDOCYTOSIS | ||||||||||||
Function / homology | ![]() 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 / melanosome / actin cytoskeleton / synaptic vesicle / Clathrin-mediated endocytosis / mitotic cell cycle / chemical synaptic transmission / protein domain specific binding / cell division / structural molecule activity / mitochondrion / extracellular exosome / identical protein binding / plasma membrane / cytosol 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 | ![]() | 317.9 KB | Display | ![]() |
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PDB format | ![]() | 259.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 477.5 KB | Display | ![]() |
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Full document | ![]() | 479.6 KB | Display | |
Data in XML | ![]() | 36.2 KB | Display | |
Data in CIF | ![]() | 55.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5m5rC ![]() 5m5tC ![]() 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: 1177.258 Da / Num. of mol.: 4 / Fragment: Clathrin-box motif, UNP residues 349-358 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.87 Å3/Da / Density % sol: 68.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1 uL protein:peptide mix (14 mg/mL NTD and 3.4 mM peptide) plus 2 uL reservoir equilibrated against a 200 uL reservoir of 0.85 M sodium malonate pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 5, 2015 / Details: toroidal mirrors |
Radiation | Monochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→67.1 Å / Num. obs: 99868 / % possible obs: 100 % / Redundancy: 5.1 % / CC1/2: 0.993 / Rmerge(I) obs: 0.149 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 1.88→1.93 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.092 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.568 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1C9I Resolution: 1.88→67.06 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.223 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.118 / 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: 23.627 Å2
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Refinement step | Cycle: 1 / Resolution: 1.88→67.06 Å
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