[English] 日本語
Yorodumi- PDB-5hb0: Crystal structure of Chaetomium thermophilum Nup170 CTD-Nup145N c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hb0 | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Chaetomium thermophilum Nup170 CTD-Nup145N complex | ||||||||||||||||||||||||||||||
Components |
| ||||||||||||||||||||||||||||||
Keywords | PROTEIN TRANSPORT / Nucleocytoplasmic transport | ||||||||||||||||||||||||||||||
Function / homology | Function and homology information protein localization to nuclear inner membrane / nuclear pore inner ring / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / telomere tethering at nuclear periphery / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / structural constituent of nuclear pore / RNA export from nucleus / nuclear localization sequence binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases ...protein localization to nuclear inner membrane / nuclear pore inner ring / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / telomere tethering at nuclear periphery / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / structural constituent of nuclear pore / RNA export from nucleus / nuclear localization sequence binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / mRNA transport / protein import into nucleus / nuclear membrane / hydrolase activity / RNA binding Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 Å | ||||||||||||||||||||||||||||||
Authors | Lin, D.H. / Mobbs, G. / 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 | 5hb0.cif.gz | 775 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5hb0.ent.gz | 656.6 KB | Display | PDB format |
PDBx/mmJSON format | 5hb0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hb0_validation.pdf.gz | 468.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5hb0_full_validation.pdf.gz | 473.9 KB | Display | |
Data in XML | 5hb0_validation.xml.gz | 65.9 KB | Display | |
Data in CIF | 5hb0_validation.cif.gz | 90.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/5hb0 ftp://data.pdbj.org/pub/pdb/validation_reports/hb/5hb0 | HTTPS FTP |
-Related structure data
Related structure data | 5haxC 5hayC 5hazC 5hb1C 5hb2C 5hb3C 5hb4C 5hb5C 5hb6C 5hb7C 5hb8C C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
6 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 61392.016 Da / Num. of mol.: 4 / Mutation: delta 1375-1377 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: NUP170, CTHT_0036270 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S7B6 #2: Protein/peptide | Mass: 2590.007 Da / Num. of mol.: 4 / Source method: obtained synthetically Source: (synth.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) References: UniProt: G0SAK3, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.43 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: 12 % (w/v) PEG 3350, 0.2 M lithium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 45493 / % possible obs: 98.8 % / Redundancy: 7 % / Net I/σ(I): 6.2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 3.5→45.364 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 30.29 / 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: 3.5→45.364 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|