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Yorodumi- PDB-5hb3: Crystal structure of Chaetomium thermophilum Nic96 SOL-Nup53 complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hb3 | ||||||||||||||||||||||||||||||
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Title | Crystal structure of Chaetomium thermophilum Nic96 SOL-Nup53 complex | ||||||||||||||||||||||||||||||
Components |
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Keywords | TRANSPORT PROTEIN / Nucleocytoplasmic Transport / Protein Transport | ||||||||||||||||||||||||||||||
Function / homology | Function and homology information structural constituent of nuclear pore / poly(A)+ mRNA export from nucleus / mRNA transport / nuclear pore / protein import into nucleus / protein transport / nuclear membrane Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.65 Å | ||||||||||||||||||||||||||||||
Authors | Lin, D.H. / Stuwe, T. / Hoelz, A. | ||||||||||||||||||||||||||||||
Funding support | United States, Germany, China, 9items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hb3.cif.gz | 537.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hb3.ent.gz | 446.3 KB | Display | PDB format |
PDBx/mmJSON format | 5hb3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/5hb3 ftp://data.pdbj.org/pub/pdb/validation_reports/hb/5hb3 | HTTPS FTP |
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-Related structure data
Related structure data | 5haxC 5hayC 5hazC 5hb0C 5hb1C 5hb2C 5hb4C 5hb5C 5hb6C 5hb7C 5hb8C C: citing same article (ref.) |
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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: Protein | Mass: 81516.734 Da / Num. of mol.: 2 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: NIC96, CTHT_0008480 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S024 #2: Protein | Mass: 5989.653 Da / Num. of mol.: 2 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: NUP53, CTHT_0012410 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S156 #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.8 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M TRIS (pH 7.0), 12 % (w/v) PEG 6000, 1.2 M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. obs: 48566 / % possible obs: 88.6 % / Redundancy: 3.9 % / Net I/σ(I): 15.1 |
-Processing
Software |
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Refinement | Resolution: 2.65→47.285 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 31.04 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→47.285 Å
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Refine LS restraints |
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LS refinement shell |
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