[English] 日本語
![](img/lk-miru.gif)
- PDB-5m61: Clathrin heavy chain N-terminal domain bound to an extended amphi... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5m61 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Clathrin heavy chain N-terminal domain bound to an extended amphiphysin clathrin-box motif | ||||||||||||
![]() |
| ||||||||||||
![]() | 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 / actin cytoskeleton / melanosome / synaptic vesicle / Clathrin-mediated endocytosis / 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 | ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Muenzner, J. / Graham, S.C. | ||||||||||||
Funding support | ![]() ![]()
| ||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 321.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 262 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5m5rC ![]() 5m5sC ![]() 5m5tC ![]() 5m5uC ![]() 5m5vC ![]() 1c9iS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
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: 1453.612 Da / Num. of mol.: 4 / Fragment: extended Clathrin-box motif, UNP residues 349-360 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density % sol: 66.44 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 1 uL protein:peptide mix (14 mg/mL protein, 3.4 mM peptide) plus 2 uL of 1.04 M sodium malonate pH 7.1, 0.2 M sodium perchlorate equilibrated against a 200 uL reservoir of 1.15 M sodium malonate pH 7.1 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 1, 2015 / Details: KB mirrors |
Radiation | Monochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→39.7 Å / Num. obs: 102809 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.84→1.89 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.232 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.528 / % possible all: 99.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1C9I Resolution: 1.84→39.66 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / SU B: 4.542 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.088 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.778 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.84→39.66 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|