+Open data
-Basic information
Entry | Database: PDB / ID: 1bpo | ||||||
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Title | CLATHRIN HEAVY-CHAIN TERMINAL DOMAIN AND LINKER | ||||||
Components | PROTEIN (CLATHRIN) | ||||||
Keywords | MEMBRANE PROTEIN / CLATHRIN ENDOCYTOSIS BETA-PROPELLER COATED-PITS | ||||||
Function / homology | Function and homology information 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 / clathrin light chain binding / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance ...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 / clathrin light chain binding / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / negative regulation of hyaluronan biosynthetic process / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / clathrin complex / clathrin coat / WNT5A-dependent internalization of FZD4 / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / amyloid-beta clearance by transcytosis / transferrin transport / MHC class II antigen presentation / extrinsic component of synaptic vesicle membrane / clathrin coat of coated pit / mitotic spindle microtubule / Recycling pathway of L1 / clathrin coat disassembly / clathrin coat assembly / photoreceptor ribbon synapse / Cargo recognition for clathrin-mediated endocytosis / clathrin-coated endocytic vesicle / Clathrin-mediated endocytosis / membrane coat / clathrin-dependent endocytosis / protein serine/threonine kinase binding / 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 / regulation of mitotic spindle organization / clathrin-coated pit / T-tubule / heat shock protein binding / receptor-mediated endocytosis / peptide binding / intracellular protein transport / clathrin-coated endocytic vesicle membrane / sarcolemma / terminal bouton / receptor internalization / spindle / autophagy / disordered domain specific binding / melanosome / double-stranded RNA binding / mitotic cell cycle / protein kinase binding / structural molecule activity / protein-containing complex / membrane / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.6 Å | ||||||
Authors | Harr, E.T. / Musacchio, A. / Harrison, S.C. / Kirchhausen, T. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1998 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bpo.cif.gz | 285.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bpo.ent.gz | 235 KB | Display | PDB format |
PDBx/mmJSON format | 1bpo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/1bpo ftp://data.pdbj.org/pub/pdb/validation_reports/bp/1bpo | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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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.) Rattus norvegicus (Norway rat) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P11442 #2: 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 | 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: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9875 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.6→6 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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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 |