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Yorodumi- PDB-7s3a: Crystal structure of intact U2AF65 RRM-region bound to AdML-C5 ol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7s3a | |||||||||
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Title | Crystal structure of intact U2AF65 RRM-region bound to AdML-C5 oligonucleotide | |||||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA/DNA / PROTEIN-RNA COMPLEX / RNA SPLICING FACTOR / RNA RECOGNITION MOTIF / POLYPYRIMIDINE TRACT / RNA BINDING PROTEIN-RNA-DNA 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 / commitment complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / 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 / commitment complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / U2-type prespliceosome / molecular function inhibitor activity / 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 processing / mRNA splicing, via spliceosome / nuclear speck / enzyme binding / RNA binding / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.48 Å | |||||||||
Authors | Jenkins, J.L. / Henderson, S. / Kielkopf, C.L. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2022 Title: Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal. Authors: Glasser, E. / Maji, D. / Biancon, G. / Puthenpeedikakkal, A.M.K. / Cavender, C.E. / Tebaldi, T. / Jenkins, J.L. / Mathews, D.H. / Halene, S. / 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 | 7s3a.cif.gz | 145.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s3a.ent.gz | 110.9 KB | Display | PDB format |
PDBx/mmJSON format | 7s3a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/7s3a ftp://data.pdbj.org/pub/pdb/validation_reports/s3/7s3a | HTTPS FTP |
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-Related structure data
Related structure data | 7s3bC 7s3cC 5ev4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22237.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: U2AF2, U2AF65 / Details (production host): PGEX-6P / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P26368 | ||||
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#2: DNA/RNA hybrid | Mass: 2448.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.21 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.60 M succinic acid, 0.10 M Hepes pH 7.0, 2% Peg MME 2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.033 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2015 Details: Rh coated collimating mirrors, K-B focusing mirrors |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→38.75 Å / Num. obs: 35972 / % possible obs: 98.7 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.026 / Rrim(I) all: 0.05 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.48→1.5 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 1368 / CC1/2: 0.951 / Rpim(I) all: 0.154 / Rrim(I) all: 0.251 / % possible all: 76.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5ev4 Resolution: 1.48→37.76 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 13.38 / 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: 79.49 Å2 / Biso mean: 23.4301 Å2 / Biso min: 10.19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.48→37.76 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17
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