[English] 日本語
Yorodumi- PDB-5hay: Crystal structure of Chaetomium thermophilum Nup170 CTD Y905M L10... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hay | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Chaetomium thermophilum Nup170 CTD Y905M L1007M L1183M V1292M mutant | ||||||||||||||||||||||||||||||
Components | Nucleoporin NUP170 | ||||||||||||||||||||||||||||||
Keywords | TRANSPORT PROTEIN / Nucleocytoplasmic transport / Protein transport | ||||||||||||||||||||||||||||||
Function / homology | Function and homology information structural constituent of nuclear pore / mRNA transport / nuclear pore / protein transport / nuclear membrane Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å | ||||||||||||||||||||||||||||||
Authors | Lin, D.H. / Fan, Y. / Hoelz, A. | ||||||||||||||||||||||||||||||
Funding support | United States, Germany, China, 9items
| ||||||||||||||||||||||||||||||
Citation | Journal: Science / Year: 2016 Title: Architecture of the symmetric core of the nuclear pore. Authors: Lin, D.H. / Stuwe, T. / Schilbach, S. / Rundlet, E.J. / Perriches, T. / Mobbs, G. / Fan, Y. / Thierbach, K. / Huber, F.M. / Collins, L.N. / Davenport, A.M. / Jeon, Y.E. / Hoelz, A. | ||||||||||||||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5hay.cif.gz | 401.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5hay.ent.gz | 344 KB | Display | PDB format |
PDBx/mmJSON format | 5hay.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/5hay ftp://data.pdbj.org/pub/pdb/validation_reports/ha/5hay | HTTPS FTP |
---|
-Related structure data
Related structure data | 5haxC 5hazC 5hb0C 5hb1C 5hb2C 5hb3C 5hb4C 5hb5C 5hb6C 5hb7C 5hb8C C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 66145.867 Da / Num. of mol.: 2 / Mutation: Y905M, L1007M, L1183M, V1292M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: NUP170, CTHT_0036270 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S7B6 #2: Chemical | ChemComp-NA / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.56 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 0.1 M MES (pH 6.3), 10 % PEG 20000, 10 % (v/v) ethylene glycol, 0.2 M potassium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 30966 / % possible obs: 98.2 % / Redundancy: 16.2 % / Net I/σ(I): 22.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.8→49.185 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.83 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→49.185 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|