+Open data
-Basic information
Entry | Database: PDB / ID: 2xzo | ||||||
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Title | Upf1 helicase - RNA complex | ||||||
Components |
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Keywords | HYDROLASE/RNA / HYDROLASE-RNA COMPLEX / NMD / RNA DEGRADATION / ALLOSTERIC REGULATION | ||||||
Function / homology | Function and homology information 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 / regulation of telomere maintenance / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / DNA duplex unwinding / telomeric DNA binding / nuclear-transcribed mRNA catabolic process / cellular response to interleukin-1 / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / helicase activity / P-body / chromosome, telomeric region / DNA replication / cellular response to lipopolysaccharide / DNA helicase / RNA helicase activity / RNA helicase / DNA repair / chromatin binding / chromatin / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.395 Å | ||||||
Authors | Chakrabarti, S. / Jayachandran, U. / Bonneau, F. / Fiorini, F. / Basquin, C. / Domcke, S. / Le Hir, H. / Conti, E. | ||||||
Citation | Journal: Mol.Cell / Year: 2011 Title: Molecular Mechanisms for the RNA-Dependent ATPase Activity of Upf1 and its Regulation by Upf2. Authors: Chakrabarti, S. / Jayachandran, U. / Bonneau, F. / Fiorini, F. / Basquin, C. / Domcke, S. / Le Hir, H. / Conti, E. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xzo.cif.gz | 141.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xzo.ent.gz | 105.1 KB | Display | PDB format |
PDBx/mmJSON format | 2xzo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xzo_validation.pdf.gz | 805.4 KB | Display | wwPDB validaton report |
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Full document | 2xzo_full_validation.pdf.gz | 814.1 KB | Display | |
Data in XML | 2xzo_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 2xzo_validation.cif.gz | 35.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/2xzo ftp://data.pdbj.org/pub/pdb/validation_reports/xz/2xzo | HTTPS FTP |
-Related structure data
Related structure data | 2xzlC 2xzpC 2wjvS 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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1 |
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Unit cell |
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-Components
-Protein / RNA chain , 2 types, 2 molecules AD
#1: Protein | Mass: 70028.406 Da / Num. of mol.: 1 / Fragment: HELICASE DOMAIN, RESIDUES 295-914 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) GOLD PLYSS / References: UniProt: Q92900, RNA helicase |
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#2: RNA chain | Mass: 2098.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
-Non-polymers , 5 types, 132 molecules
#3: Chemical | #4: Chemical | ChemComp-ADP / | #5: Chemical | ChemComp-ALF / | #6: Chemical | #7: 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: 2.48 Å3/Da / Density % sol: 50.39 % / Description: NONE |
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Crystal grow | pH: 4.6 / Details: 100 MM SODIUM ACETATE PH 4.6, 20 MM CACL2, 15% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2010 / Details: LN2-COOLED DYNAMICALLY BENDABLE MIRROR |
Radiation | Monochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→49.18 Å / Num. obs: 35441 / % possible obs: 99.8 % / Observed criterion σ(I): 3.3 / Redundancy: 6.2 % / Biso Wilson estimate: 39.78 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.4→2.52 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.3 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WJV Resolution: 2.395→49.184 Å / SU ML: 0.37 / σ(F): 1.36 / Phase error: 22.96 / Stereochemistry target values: ML Details: RESIDUES 349-354 ARE DISORDERED. RESIDUES 582-585 ARE DISORDERED
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.935 Å2 / ksol: 0.302 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.395→49.184 Å
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Refine LS restraints |
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LS refinement shell |
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