+Open data
-Basic information
Entry | Database: PDB / ID: 6qnp | |||||||||
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Title | CLATHRIN HEAVY CHAIN N-TERMINAL DOMAIN BOUND TO GTSE1 LIDL MOTIF | |||||||||
Components |
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Keywords | CELL CYCLE / BETA-PROPELLER / CLATHRIN-BOX / LIDL-MOTIF | |||||||||
Function / homology | Function and homology information clathrin coat of trans-Golgi network vesicle / clathrin light chain binding / negative regulation of hyaluronan biosynthetic process / clathrin complex / clathrin coat / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Entry of Influenza Virion into Host Cell via Endocytosis / transferrin transport / amyloid-beta clearance by transcytosis ...clathrin coat of trans-Golgi network vesicle / clathrin light chain binding / negative regulation of hyaluronan biosynthetic process / clathrin complex / clathrin coat / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Entry of Influenza Virion into Host Cell via Endocytosis / transferrin transport / amyloid-beta clearance by transcytosis / mitotic spindle microtubule / clathrin coat of coated pit / clathrin coat disassembly / clathrin coat assembly / Retrograde neurotrophin signalling / Formation of annular gap junctions / clathrin-coated endocytic vesicle / Gap junction degradation / LDL clearance / clathrin-dependent endocytosis / ALK mutants bind TKIs / endolysosome membrane / retrograde transport, endosome to Golgi / negative regulation of protein localization to plasma membrane / clathrin-coated vesicle / Lysosome Vesicle Biogenesis / RHOV GTPase cycle / low-density lipoprotein particle receptor binding / Golgi Associated Vesicle Biogenesis / ubiquitin-specific protease binding / Recycling pathway of L1 / cytoplasmic microtubule / microtubule-based process / RHOU GTPase cycle / EPH-ephrin mediated repulsion of cells / regulation of mitotic spindle organization / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / MHC class II antigen presentation / VLDLR internalisation and degradation / receptor-mediated endocytosis / trans-Golgi network membrane / G2/M Checkpoints / intracellular protein transport / clathrin-coated endocytic vesicle membrane / receptor internalization / mitotic spindle / autophagy / spindle / osteoblast differentiation / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / double-stranded RNA binding / disordered domain specific binding / extracellular vesicle / Signaling by ALK fusions and activated point mutants / melanosome / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / mitotic cell cycle / microtubule binding / lysosome / endosome / cell division / focal adhesion / protein kinase binding / structural molecule activity / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å | |||||||||
Authors | Porfetye, A.T. / Lin, Y. / Vetter, I.R. | |||||||||
Citation | Journal: J.Cell Biol. / Year: 2020 Title: Clathrin's adaptor interaction sites are repurposed to stabilize microtubules during mitosis. Authors: Rondelet, A. / Lin, Y.C. / Singh, D. / Porfetye, A.T. / Thakur, H.C. / Hecker, A. / Brinkert, P. / Schmidt, N. / Bendre, S. / Muller, F. / Mazul, L. / Widlund, P.O. / Bange, T. / Hiller, M. ...Authors: Rondelet, A. / Lin, Y.C. / Singh, D. / Porfetye, A.T. / Thakur, H.C. / Hecker, A. / Brinkert, P. / Schmidt, N. / Bendre, S. / Muller, F. / Mazul, L. / Widlund, P.O. / Bange, T. / Hiller, M. / Vetter, I.R. / Bird, A.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qnp.cif.gz | 305.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qnp.ent.gz | 246.2 KB | Display | PDB format |
PDBx/mmJSON format | 6qnp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qnp_validation.pdf.gz | 481.2 KB | Display | wwPDB validaton report |
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Full document | 6qnp_full_validation.pdf.gz | 497.6 KB | Display | |
Data in XML | 6qnp_validation.xml.gz | 55.1 KB | Display | |
Data in CIF | 6qnp_validation.cif.gz | 75.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/6qnp ftp://data.pdbj.org/pub/pdb/validation_reports/qn/6qnp | HTTPS FTP |
-Related structure data
Related structure data | 6qnnC 5m5tS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 40543.516 Da / Num. of mol.: 4 Fragment: LIDL motifs A-D, REFSEQ RESIDUES 653-719, N-TERMINAL 'GPLGS' ARE NON-NATURAL Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLTC, CLH17, CLTCL2, KIAA0034 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00610 #2: Protein | Mass: 7040.994 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTSE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NYZ3 #3: Water | ChemComp-HOH / | |
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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: 2.39 Å3/Da / Density % sol: 40.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: 12% PEG 4000, 0.1M SODIUM ACETATE, 0.1M HEPES pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97793 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 8, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97793 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→49.19 Å / Num. obs: 43602 / % possible obs: 99.2 % / Redundancy: 6.876 % / Biso Wilson estimate: 65.226 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.141 / Rrim(I) all: 0.153 / Χ2: 1.002 / Net I/σ(I): 10.39 / Num. measured all: 299788 / Scaling rejects: 47 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5M5T Resolution: 2.7→49.19 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.12
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.64 Å2 / Biso mean: 71.1235 Å2 / Biso min: 29.26 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→49.19 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16
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