+Open data
-Basic information
Entry | Database: PDB / ID: 3rw6 | ||||||
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Title | Structure of nuclear RNA export factor TAP bound to CTE RNA | ||||||
Components |
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Keywords | TRANSPORT PROTEIN/RNA / retroviral constitutive transport element (CTE) / RNA recognition motif (RRM) / leucine-rich repeat (LRR) motif / TRANSPORT PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information nuclear RNA export factor complex / nuclear inclusion body / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / poly(A)+ mRNA export from nucleus / mRNA export from nucleus / nuclear pore / cytoplasmic stress granule ...nuclear RNA export factor complex / nuclear inclusion body / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / poly(A)+ mRNA export from nucleus / mRNA export from nucleus / nuclear pore / cytoplasmic stress granule / protein transport / nuclear speck / mRNA binding / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Teplova, M. / Khin, N.W. / Patel, D.J. / Izaurralde, E. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2011 Title: Structure-function studies of nucleocytoplasmic transport of retroviral genomic RNA by mRNA export factor TAP. Authors: Teplova, M. / Wohlbold, L. / Khin, N.W. / Izaurralde, E. / Patel, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rw6.cif.gz | 184.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rw6.ent.gz | 139.7 KB | Display | PDB format |
PDBx/mmJSON format | 3rw6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/3rw6 ftp://data.pdbj.org/pub/pdb/validation_reports/rw/3rw6 | HTTPS FTP |
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-Related structure data
Related structure data | 3rw7SC S: Starting model for refinement 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: 30509.930 Da / Num. of mol.: 2 / Fragment: unp residues 96-362 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NXF1, TAP, TAP (NXF1) / Plasmid: T7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UBU9 #2: RNA chain | Mass: 20284.963 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: enzymatic synthesis #3: Water | ChemComp-HOH / | |
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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: 2.6 Å3/Da / Density % sol: 52.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 2 M ammonium acetate, 0.1 M Na acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 44640 / % possible obs: 96.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.074 / Χ2: 1.03 / Net I/σ(I): 17.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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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: pdb entry 3RW7 and an idealized A-form RNA 7-nt duplex Resolution: 2.3→37.866 Å / Occupancy max: 1 / Occupancy min: 0.45 / SU ML: 0.37 / σ(F): 0.09 / Phase error: 30.65 / 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 / Bsol: 22.263 Å2 / ksol: 0.285 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.6 Å2 / Biso mean: 48.4009 Å2 / Biso min: 19.26 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→37.866 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16
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