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Yorodumi- PDB-3lvg: Crystal structure of a clathrin heavy chain and clathrin light ch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lvg | ||||||
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Title | Crystal structure of a clathrin heavy chain and clathrin light chain complex | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / self assembly / Coated pit / Cytoplasmic vesicle / Membrane / Calcium | ||||||
Function / homology | Function and homology information postsynaptic endocytic zone cytoplasmic component / 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 ...postsynaptic endocytic zone cytoplasmic component / 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 / clathrin vesicle coat / Lysosome Vesicle Biogenesis / clathrin light chain binding / negative regulation of hyaluronan biosynthetic process / clathrin complex / clathrin coat / MHC class II antigen presentation / VLDLR internalisation and degradation / clathrin heavy chain binding / clathrin coat of coated pit / Cargo recognition for clathrin-mediated endocytosis / clathrin coat disassembly / clathrin coat assembly / clathrin-coated endocytic vesicle / membrane coat / Clathrin-mediated endocytosis / clathrin-dependent endocytosis / arrestin family protein binding / ciliary membrane / receptor-mediated endocytosis / intracellular protein transport / trans-Golgi network / synaptic vesicle membrane / spindle / autophagy / disordered domain specific binding / melanosome / mitotic cell cycle / cell division / protein domain specific binding / structural molecule activity / mitochondrion / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 7.94 Å | ||||||
Authors | Wilbur, J.D. / Hwang, P.K. / Ybe, J.A. / Lane, M. / Sellers, B.D. / Jacobson, M.P. / Fletterick, R.J. / Brodsky, F.M. | ||||||
Citation | Journal: Dev.Cell / Year: 2010 Title: Conformation switching of clathrin light chain regulates clathrin lattice assembly. Authors: Wilbur, J.D. / Hwang, P.K. / Ybe, J.A. / Lane, M. / Sellers, B.D. / Jacobson, M.P. / Fletterick, R.J. / Brodsky, F.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lvg.cif.gz | 371.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lvg.ent.gz | 287 KB | Display | PDB format |
PDBx/mmJSON format | 3lvg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/3lvg ftp://data.pdbj.org/pub/pdb/validation_reports/lv/3lvg | HTTPS FTP |
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-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: 72180.977 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: CLTC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P49951 #2: Protein | Mass: 19147.379 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: CLTB, CLTLB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04975 Sequence details | FULL-LENGTH CLATHRIN LIGHT CHAIN B WAS USED IN THE CRYSTALLIZATION EXPERIMENT (UNIPROT ID P04975, ...FULL-LENGTH CLATHRIN LIGHT CHAIN B WAS USED IN THE CRYSTALLIZ | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 200mM citrate, 16-22% glycerol, 2% trifluoroethanol, vapor diffusion, hanging drop, temperature 298K PH range: 4.0-5.0 |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.017 Å |
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Detector | Detector: CCD / Date: Mar 3, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.017 Å / Relative weight: 1 |
Reflection | Resolution: 7.9→250 Å / Num. obs: 10700 / Redundancy: 9 % / Rsym value: 0.075 / Net I/σ(I): 20 |
Reflection shell | Resolution: 7.9→8.55 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 2079 / Rsym value: 0.882 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 7.94→100 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 Details: Due to the low resolution the side chain positions of UNK residues are undetermined though they were present in the phasing and refinement of the structure. Reflection data was processed ...Details: Due to the low resolution the side chain positions of UNK residues are undetermined though they were present in the phasing and refinement of the structure. Reflection data was processed using multiple resolution cutoffs. Initially, the highest resolution was 8.3A. To determine the best resolution for structure determination, maps were calculated with molecular replacement phases and manually inspected for increased structural details. For this manual determination of the resolution data was processed up to 5A resolution in an attempt to gain the highest resolution possible. The reflection data used for structure refinement was cutoff at 7.9A. Reflection data processed to a variety of other high resolution cutoffs can be obtained by sending a request to the authors.
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Solvent computation | Bsol: 164.754 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 350.12 Å2 / Biso mean: 295.198 Å2 / Biso min: 232.2 Å2
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Refinement step | Cycle: LAST / Resolution: 7.94→100 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: protein_rep.param |