+Open data
-Basic information
Entry | Database: PDB / ID: 5ev1 | ||||||
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Title | Structure I of Intact U2AF65 Recognizing a 3' Splice Site Signal | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / PROTEIN-RNA COMPLEX / RNA SPLICING FACTOR / RNA RECOGNITION MOTIF / POLYPYRIMIDINE TRACT / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / mRNA 3'-end processing / C2H2 zinc finger domain binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / commitment complex / RNA Polymerase II Transcription Termination / U2-type prespliceosome / molecular function inhibitor activity ...U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / mRNA 3'-end processing / C2H2 zinc finger domain binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / commitment complex / RNA Polymerase II Transcription Termination / U2-type prespliceosome / molecular function inhibitor activity / spliceosomal complex assembly / Protein hydroxylation / negative regulation of mRNA splicing, via spliceosome / negative regulation of protein ubiquitination / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / nuclear speck / enzyme binding / RNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.037 Å | ||||||
Authors | Agrawal, A.A. / Jenkins, J.L. / Kielkopf, C.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2016 Title: An extended U2AF(65)-RNA-binding domain recognizes the 3' splice site signal. Authors: Agrawal, A.A. / Salsi, E. / Chatrikhi, R. / Henderson, S. / Jenkins, J.L. / Green, M.R. / Ermolenko, D.N. / Kielkopf, C.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ev1.cif.gz | 96.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ev1.ent.gz | 71.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ev1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ev1_validation.pdf.gz | 458.4 KB | Display | wwPDB validaton report |
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Full document | 5ev1_full_validation.pdf.gz | 460.8 KB | Display | |
Data in XML | 5ev1_validation.xml.gz | 12 KB | Display | |
Data in CIF | 5ev1_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/5ev1 ftp://data.pdbj.org/pub/pdb/validation_reports/ev/5ev1 | HTTPS FTP |
-Related structure data
Related structure data | 5ev2C 5ev3C 5ev4C 2g4bS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
-Protein / DNA/RNA hybrid , 2 types, 2 molecules AB
#1: Protein | Mass: 21970.004 Da / Num. of mol.: 1 / Fragment: UNP residues 141-341 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: U2AF2, U2AF65 / Plasmid: PGEX-6P / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P26368 |
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#2: DNA/RNA hybrid | Mass: 2725.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The 3' U is disordered in this 9mer / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 122 molecules
#3: Chemical | #4: Chemical | ChemComp-PGE / | #5: Chemical | ChemComp-PEG / | #6: 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: 2.27 Å3/Da / Density % sol: 45.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 100 mM phosphate-citrate buffer, 40% Peg400, 10% dioxane PH range: 4.2 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97945 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.037→32.456 Å / Num. obs: 13202 / % possible obs: 95.5 % / Redundancy: 4.6 % / Biso Wilson estimate: 35.26 Å2 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.019 / Rrim(I) all: 0.044 / Net I/av σ(I): 13.688 / Net I/σ(I): 21.2 / Num. measured all: 61150 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2G4B Resolution: 2.037→32.456 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0.89 / Phase error: 26.13 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 130.23 Å2 / Biso mean: 47.2807 Å2 / Biso min: 20.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.037→32.456 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: 14
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