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Yorodumi- PDB-1c9l: PEPTIDE-IN-GROOVE INTERACTIONS LINK TARGET PROTEINS TO THE B-PROP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c9l | ||||||
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Title | PEPTIDE-IN-GROOVE INTERACTIONS LINK TARGET PROTEINS TO THE B-PROPELLER OF CLATHRIN | ||||||
Components |
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Keywords | ENDOCYTOSIS/EXOCYTOSIS / BETA-PROPELLER / HELICAL HAIRPIN / ENDOCYTOSIS-EXOCYTOSIS COMPLEX | ||||||
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 / 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 / clathrin coat of coated pit / mitotic spindle microtubule / 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 / clathrin-coated endocytic vesicle membrane / intracellular protein transport / terminal bouton / receptor internalization / sarcolemma / autophagy / spindle / disordered domain specific binding / double-stranded RNA binding / melanosome / 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 / Resolution: 2.9 Å | ||||||
Authors | ter Haar, E. / Harrison, S.C. / Kirchhausen, T. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Peptide-in-groove interactions link target proteins to the beta-propeller of clathrin. Authors: ter Haar, E. / 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 | 1c9l.cif.gz | 148.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c9l.ent.gz | 118.4 KB | Display | PDB format |
PDBx/mmJSON format | 1c9l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c9l_validation.pdf.gz | 456 KB | Display | wwPDB validaton report |
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Full document | 1c9l_full_validation.pdf.gz | 485.8 KB | Display | |
Data in XML | 1c9l_validation.xml.gz | 29.8 KB | Display | |
Data in CIF | 1c9l_validation.cif.gz | 39.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/1c9l ftp://data.pdbj.org/pub/pdb/validation_reports/c9/1c9l | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39751.605 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PBAT4 / Production host: Escherichia coli (E. coli) / References: UniProt: P11442 #2: Protein/peptide | Mass: 980.027 Da / Num. of mol.: 2 / Fragment: CLATHRIN-BOX PEPTIDE / Source method: obtained synthetically Details: This peptide was chemically sythesized.The sequence of this peptide naturally occurs in humans (HOMO SAPIENS). |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.91 Å3/Da / Density % sol: 68.55 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 400, KOAc, DTT, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.54 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. all: 27854 / Num. obs: 27854 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.2 % / Biso Wilson estimate: 220.3 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 5 % / Rmerge(I) obs: 0.146 / % possible all: 88.4 |
Reflection shell | *PLUS % possible obs: 88.4 % |
-Processing
Software |
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Refinement | Resolution: 2.9→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1585264.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.79 Å2 / ksol: 0.371 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PA / Topol file: PROTEIN.TOP | |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.22 / Rfactor Rwork: 0.22 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |