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- PDB-2gk7: Structural and Functional insights into the human Upf1 helicase core -
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Open data
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Basic information
Entry | Database: PDB / ID: 2gk7 | ||||||
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Title | Structural and Functional insights into the human Upf1 helicase core | ||||||
![]() | Regulator of nonsense transcripts 1 | ||||||
![]() | HYDROLASE / Upf1 / helicase / NMD | ||||||
Function / homology | ![]() double-stranded DNA helicase activity / supraspliceosomal complex / positive regulation of mRNA cis splicing, via spliceosome / exon-exon junction complex / telomere maintenance via semi-conservative replication / positive regulation of mRNA catabolic process / cell cycle phase transition / regulation of translational termination / histone mRNA catabolic process / 3'-UTR-mediated mRNA destabilization ...double-stranded DNA helicase activity / supraspliceosomal complex / positive regulation of mRNA cis splicing, via spliceosome / exon-exon junction complex / telomere maintenance via semi-conservative replication / positive regulation of mRNA catabolic process / cell cycle phase transition / regulation of translational termination / histone mRNA catabolic process / 3'-UTR-mediated mRNA destabilization / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / regulation of telomere maintenance / DNA duplex unwinding / nuclear-transcribed mRNA catabolic process / telomeric DNA binding / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / cellular response to interleukin-1 / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / helicase activity / P-body / cellular response to lipopolysaccharide / DNA replication / DNA helicase / chromosome, telomeric region / RNA helicase activity / RNA helicase / DNA repair / chromatin binding / protein-containing complex binding / chromatin / perinuclear region of cytoplasm / ATP hydrolysis activity / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Cheng, Z. / Muhlrad, D. / Parker, R. / Song, H. | ||||||
![]() | ![]() Title: Structural and functional insights into the human Upf1 helicase core Authors: Cheng, Z. / Muhlrad, D. / Lim, M.K. / Parker, R. / Song, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.9 KB | Display | ![]() |
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PDB format | ![]() | 101 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.1 KB | Display | ![]() |
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Full document | ![]() | 463.1 KB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 33.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2gjkSC ![]() 2gk6C ![]() 2gk8 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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Unit cell |
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Components
#1: Protein | Mass: 70056.422 Da / Num. of mol.: 1 / Fragment: helicase core domain(residues 295-914) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q92900, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.18 % |
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Crystal grow | Temperature: 295 K / Method: evaporation / pH: 5.8 Details: 100mM Na/K Phosphate, 6-8% PEG3350, 10mM DTT, pH 5.8, EVAPORATION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 20, 2005 |
Radiation | Monochromator: GRAPHATE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 24896 / % possible obs: 100 % |
Reflection shell | Resolution: 2.8→2.87 Å / % possible all: 100 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() ![]() Starting model: 2GJK Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.889 / SU B: 43.334 / SU ML: 0.394 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.133 / ESU R Free: 0.404 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.622 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.871 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 75.007 Å / Origin y: 33.975 Å / Origin z: 6.8122 Å
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Refinement TLS group |
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