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Open data
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Basic information
Entry | Database: PDB / ID: 1bpo | ||||||
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Title | CLATHRIN HEAVY-CHAIN TERMINAL DOMAIN AND LINKER | ||||||
![]() | PROTEIN (CLATHRIN) | ||||||
![]() | MEMBRANE PROTEIN / CLATHRIN ENDOCYTOSIS BETA-PROPELLER COATED-PITS | ||||||
Function / homology | ![]() RHOU GTPase cycle / RHOV GTPase cycle / clathrin coat of trans-Golgi network vesicle / Gap junction degradation / Formation of annular gap junctions / presynaptic endocytic zone membrane / Myb complex / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / clathrin light chain binding ...RHOU GTPase cycle / RHOV GTPase cycle / clathrin coat of trans-Golgi network vesicle / Gap junction degradation / Formation of annular gap junctions / presynaptic endocytic zone membrane / Myb complex / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / clathrin light chain binding / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / negative regulation of hyaluronan biosynthetic process / clathrin complex / WNT5A-dependent internalization of FZD4 / clathrin coat / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / transferrin transport / MHC class II antigen presentation / amyloid-beta clearance by transcytosis / mitotic spindle microtubule / clathrin coat of coated pit / extrinsic component of synaptic vesicle membrane / Recycling pathway of L1 / clathrin coat disassembly / clathrin coat assembly / Cargo recognition for clathrin-mediated endocytosis / clathrin-coated endocytic vesicle / Clathrin-mediated endocytosis / photoreceptor ribbon synapse / membrane coat / clathrin-dependent endocytosis / retrograde transport, endosome to Golgi / negative regulation of protein localization to plasma membrane / clathrin-coated vesicle / ankyrin binding / low-density lipoprotein particle receptor binding / ubiquitin-specific protease binding / Golgi organization / synaptic vesicle endocytosis / mitotic spindle assembly / protein serine/threonine kinase binding / clathrin-coated pit / regulation of mitotic spindle organization / T-tubule / heat shock protein binding / receptor-mediated endocytosis / peptide binding / intracellular protein transport / clathrin-coated endocytic vesicle membrane / receptor internalization / terminal bouton / sarcolemma / autophagy / spindle / double-stranded RNA binding / disordered domain specific binding / melanosome / mitotic cell cycle / protein kinase binding / structural molecule activity / protein-containing complex / extracellular exosome / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Harr, E.T. / Musacchio, A. / Harrison, S.C. / Kirchhausen, T. | ||||||
![]() | ![]() Title: Atomic structure of clathrin: a beta propeller terminal domain joins an alpha zigzag linker. Authors: Haar, E.T. / Musacchio, A. / Harrison, S.C. / Kirchhausen, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 285.4 KB | Display | ![]() |
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PDB format | ![]() | 235 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 393.8 KB | Display | ![]() |
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Full document | ![]() | 501.1 KB | Display | |
Data in XML | ![]() | 42.8 KB | Display | |
Data in CIF | ![]() | 62.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 55090.168 Da / Num. of mol.: 3 / Fragment: TERMINAL DOMAIN AND LINKER Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.04 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9875 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→100 Å / Num. obs: 62332 / % possible obs: 95 % / Redundancy: 3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 10 |
Reflection | *PLUS Lowest resolution: 100 Å / Num. obs: 62848 / % possible obs: 96 % / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS % possible obs: 70 % / Rmerge(I) obs: 0.261 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.6→6 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 2.1 |