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Yorodumi- PDB-5cws: Crystal structure of the intact Chaetomium thermophilum Nsp1-Nup4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cws | ||||||||||||||||||
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Title | Crystal structure of the intact Chaetomium thermophilum Nsp1-Nup49-Nup57 channel nucleoporin heterotrimer bound to its Nic96 nuclear pore complex attachment site | ||||||||||||||||||
Components |
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Keywords | PROTEIN TRANSPORT / nucleocytoplasmic transport | ||||||||||||||||||
Function / homology | Function and homology information structural constituent of nuclear pore / nuclear localization sequence binding / mRNA transport / nuclear pore / protein transport / nuclear membrane Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) Chaetomium thermophilum (fungus) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 3.77 Å | ||||||||||||||||||
Authors | Bley, C.J. / Petrovic, S. / Paduch, M. / Lu, V. / Kossiakoff, A.A. / Hoelz, A. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: Science / Year: 2015 Title: Architecture of the fungal nuclear pore inner ring complex. Authors: Stuwe, T. / Bley, C.J. / Thierbach, K. / Petrovic, S. / Schilbach, S. / Mayo, D.J. / Perriches, T. / Rundlet, E.J. / Jeon, Y.E. / Collins, L.N. / Huber, F.M. / Lin, D.H. / Paduch, M. / ...Authors: Stuwe, T. / Bley, C.J. / Thierbach, K. / Petrovic, S. / Schilbach, S. / Mayo, D.J. / Perriches, T. / Rundlet, E.J. / Jeon, Y.E. / Collins, L.N. / Huber, F.M. / Lin, D.H. / Paduch, M. / Koide, A. / Lu, V. / Fischer, J. / Hurt, E. / Koide, S. / Kossiakoff, A.A. / Hoelz, A. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cws.cif.gz | 781.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cws.ent.gz | 667.2 KB | Display | PDB format |
PDBx/mmJSON format | 5cws.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cw/5cws ftp://data.pdbj.org/pub/pdb/validation_reports/cw/5cws | HTTPS FTP |
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-Related structure data
Related structure data | 4jnuC 4jnvC 4jo7C 4jo9C 4jq5C 5cwtC 5cwuC 5cwvC 5cwwC 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
-Protein , 4 types, 8 molecules CIDJEKFL
#3: Protein | Mass: 23558.211 Da / Num. of mol.: 2 / Fragment: UNP residues 467-674 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: NSP1, CTHT_0054390 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SBQ3 #4: Protein | Mass: 24536.504 Da / Num. of mol.: 2 / Fragment: UNP residues 246-470 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: NUP49, CTHT_0031980 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S4X2 #5: Protein | Mass: 28792.684 Da / Num. of mol.: 2 / Fragment: UNP residues 74-319 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: NUP57, CTHT_0010940 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S0R2 #6: Protein | Mass: 7793.831 Da / Num. of mol.: 2 / Fragment: UNP residues 139-211 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 |
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-Antibody , 2 types, 4 molecules AGBH
#1: Antibody | Mass: 25394.451 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #2: Antibody | Mass: 28606.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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-Non-polymers , 1 types, 2 molecules
#7: Chemical |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.85 Å3/Da / Density % sol: 68.07 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 0.1M TRIS, pH 8.7 5.7 % (w/v) PEG 20,000 1 % (v/v) 1-propanol PH range: 8.7 - 8.9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.14 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.14 Å / Relative weight: 1 |
Reflection | Resolution: 3.77→50 Å / Num. obs: 43896 / % possible obs: 99.9 % / Redundancy: 40.2 % / Rmerge(I) obs: 0.204 / Net I/σ(I): 17 |
Reflection shell | Highest resolution: 3.77 Å |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 3.77→49.666 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.79 / 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: 3.77→49.666 Å
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Refine LS restraints |
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LS refinement shell |
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