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- PDB-6b4e: Crystal structure of Saccharomyces cerevisiae Gle1 CTD-Nup42 GBM ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6b4e | |||||||||||||||||||||
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Title | Crystal structure of Saccharomyces cerevisiae Gle1 CTD-Nup42 GBM complex | |||||||||||||||||||||
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![]() | TRANSPORT PROTEIN / Complex / Nuclear Pore Complex / mRNA export / DEAD-box helicase | |||||||||||||||||||||
Function / homology | ![]() cellular response to salt stress / mRNA export from nucleus in response to heat stress / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / regulation of translational termination / tRNA export from nucleus / inositol hexakisphosphate binding / nuclear pore cytoplasmic filaments / Transport of Mature mRNA derived from an Intron-Containing Transcript / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery ...cellular response to salt stress / mRNA export from nucleus in response to heat stress / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / regulation of translational termination / tRNA export from nucleus / inositol hexakisphosphate binding / nuclear pore cytoplasmic filaments / Transport of Mature mRNA derived from an Intron-Containing Transcript / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / structural constituent of nuclear pore / regulation of translational initiation / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / NLS-bearing protein import into nucleus / mRNA export from nucleus / nuclear pore / enzyme activator activity / translation initiation factor binding / mRNA processing / phospholipid binding / transcription corepressor activity / protein transport / nuclear envelope / nuclear membrane / mitochondrion / nucleus / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Lin, D.H. / Correia, A.R. / Cai, S.W. / Huber, F.M. / Jette, C.A. / Hoelz, A. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and functional analysis of mRNA export regulation by the nuclear pore complex. Authors: Lin, D.H. / Correia, A.R. / Cai, S.W. / Huber, F.M. / Jette, C.A. / Hoelz, A. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 490.3 KB | Display | ![]() |
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PDB format | ![]() | 418.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.6 KB | Display | ![]() |
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Full document | ![]() | 485 KB | Display | |
Data in XML | ![]() | 32.8 KB | Display | |
Data in CIF | ![]() | 50.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6b4fC ![]() 6b4gC ![]() 6b4hC ![]() 6b4iC ![]() 6b4jC ![]() 6b4kC ![]() 3rrnS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 34258.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: GLE1, BRR3, RSS1, YDL207W, D1049 / Production host: ![]() ![]() #2: Protein/peptide | Mass: 4076.666 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: NUP42, RIP1, UIP1, YDR192C, YD9346.04C / Production host: ![]() ![]() #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.17 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES pH 8.2, 11 % (w/v/) PEG 3350, 0.2 M L-Proline |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→47.3 Å / Num. obs: 85335 / % possible obs: 99.3 % / Redundancy: 21.8 % / CC1/2: 0.999 / Rpim(I) all: 0.025 / Rsym value: 0.124 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 7866 / CC1/2: 0.573 / Rpim(I) all: 0.398 / Rsym value: 1.27 / % possible all: 93.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3RRN Resolution: 1.75→47.299 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.41 / 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: 1.75→47.299 Å
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Refine LS restraints |
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LS refinement shell |
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