+
Open data
-
Basic information
Entry | Database: PDB / ID: 2g4b | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of U2AF65 variant with polyuridine tract | ||||||
![]() |
| ||||||
![]() | RNA Binding Protein/RNA / protein-RNA complex / RNA splicing factor / RNA recognition motif / RNA Binding Protein-RNA COMPLEX | ||||||
Function / homology | ![]() 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 / 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 processing / mRNA splicing, via spliceosome / nuclear speck / enzyme binding / RNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sickmier, E.A. / Kielkopf, C.L. | ||||||
![]() | ![]() Title: Structural basis of polypyrimidine tract recognition by the essential splicing factor U2AF65. Authors: Sickmier, E.A. / Frato, K.E. / Paranawithana, S. / Shen, H. / Green, M.R. / Kielkopf, C.L. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2006 Title: Crystallization and preliminary X-ray analysis of a U2AF65 variant in complex with a polypyrimidine-tract analogue by use of protein engineering. Authors: Sickmier, E.A. / Frato, K.E. / Kielkopf, C.L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 51.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 36.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 463.8 KB | Display | |
Data in XML | ![]() | 9.9 KB | Display | |
Data in CIF | ![]() | 12.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fzr S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | The second part of the biological assembly is generated by the following six-fold axis: MATRIX 0.5001393 0.8659449 0.0003453 -0.8659446 0.5001394 -0.0007568 -0.0008280 0.0000795 0.9999996 TRANSLATION 129.3170471 -0.0240173 -10.3325310 |
-
Components
#1: RNA chain | Mass: 2098.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: polypyrimidine tract |
---|---|
#2: Protein | Mass: 18921.586 Da / Num. of mol.: 1 / Fragment: RNA binding domain / Mutation: deletion of residues 238-258 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-DIO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 65.83 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: .6 M ammonium sulfate, 100 mM 2-(N-morpholino) ethanesulfonic acid, sodium salt (MES) pH 6.5, 10% dioxane, 200 mM non-detergent sulfobetaine (NDSB) 195 , VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 6, 2005 |
Radiation | Monochromator: parabolic collimating mirror placed upstream of the monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 11182 / Num. obs: 11182 / % possible obs: 99.7 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 |
Reflection shell | Resolution: 2.5→2.59 Å / % possible all: 99.7 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB Entry: 2FZR ![]() 2fzr Resolution: 2.5→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
| ||||||||||||||||||||
Refine LS restraints |
|