+Open data
-Basic information
Entry | Database: PDB / ID: 4fxx | ||||||
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Title | Structure of SF1 coiled-coil domain | ||||||
Components | Splicing factor 1 | ||||||
Keywords | RNA BINDING PROTEIN / splicing factor 1 / coiled-coil / pre-mRNA splicing / U2AF65-UHM binding | ||||||
Function / homology | Function and homology information nuclear body organization / U2AF complex / regulation of steroid biosynthetic process / Leydig cell differentiation / male sex determination / regulation of mRNA splicing, via spliceosome / spliceosomal complex assembly / mRNA 3'-splice site recognition / mRNA Splicing - Major Pathway / negative regulation of smooth muscle cell proliferation ...nuclear body organization / U2AF complex / regulation of steroid biosynthetic process / Leydig cell differentiation / male sex determination / regulation of mRNA splicing, via spliceosome / spliceosomal complex assembly / mRNA 3'-splice site recognition / mRNA Splicing - Major Pathway / negative regulation of smooth muscle cell proliferation / spliceosomal complex / mRNA splicing, via spliceosome / transcription corepressor activity / nuclear body / ribosome / mRNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4801 Å | ||||||
Authors | Gupta, A. / Bauer, W.J. / Wang, W. / Kielkopf, C.L. | ||||||
Citation | Journal: Structure / Year: 2013 Title: Structure of Phosphorylated SF1 Bound to U2AF(65) in an Essential Splicing Factor Complex. Authors: Wang, W. / Maucuer, A. / Gupta, A. / Manceau, V. / Thickman, K.R. / Bauer, W.J. / Kennedy, S.D. / Wedekind, J.E. / Green, M.R. / 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 | 4fxx.cif.gz | 87.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fxx.ent.gz | 67.1 KB | Display | PDB format |
PDBx/mmJSON format | 4fxx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/4fxx ftp://data.pdbj.org/pub/pdb/validation_reports/fx/4fxx | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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-Components
#1: Protein | Mass: 12762.532 Da / Num. of mol.: 4 / Fragment: UNP Residues 26-132 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SF1, ZFM1, ZNF162 / Plasmid: pGEX-6p / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: Q15637 #2: Chemical | ChemComp-IMD / #3: Chemical | #4: 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: 2.47 Å3/Da / Density % sol: 50.11 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.34 M sodium malonate pH 6.0, 0.1 M imidazole maleate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9794 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 15, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.48→48 Å / Num. all: 18175 / Num. obs: 16211 / % possible obs: 89.19 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.08 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 10.5645 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4801→34.966 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7967 / SU ML: 0.87 / σ(F): 0 / Phase error: 27.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.151 Å2 / ksol: 0.379 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 117.25 Å2 / Biso mean: 46.2666 Å2 / Biso min: 11.78 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4801→34.966 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: 9
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