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- PDB-5kw6: Two Tandem RRM Domains of PUF60 Bound to an AdML Pre-mRNA 3' Spli... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5kw6 | |||||||||
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Title | Two Tandem RRM Domains of PUF60 Bound to an AdML Pre-mRNA 3' Splice Site Analogue with a Modified Binding-Site Nucleic Acid Base | |||||||||
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![]() | splicing/dna / TANDEM RRMS / PROTEIN-NUCLEIC ACID COMPLEX / SPLICING FACTOR / splicing-dna complex | |||||||||
Function / homology | ![]() alternative mRNA splicing, via spliceosome / mRNA splice site recognition / precatalytic spliceosome / regulation of alternative mRNA splicing, via spliceosome / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / cell junction / cadherin binding / apoptotic process / DNA binding ...alternative mRNA splicing, via spliceosome / mRNA splice site recognition / precatalytic spliceosome / regulation of alternative mRNA splicing, via spliceosome / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / cell junction / cadherin binding / apoptotic process / DNA binding / RNA binding / nucleoplasm / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Crichlow, G.V. / Hsiao, H.-H. / Albright, R. / Lolis, E.J. / Braddock, D.T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Unraveling the mechanism of recognition of the 3' splice site of the adenovirus major late promoter intron by the alternative splicing factor PUF60. Authors: Hsiao, H.T. / Crichlow, G.V. / Murphy, J.W. / Folta-Stogniew, E.J. / Lolis, E.J. / Braddock, D.T. #1: ![]() Title: Dimerization of FIR upon FUSE DNA binding suggests a mechanism of c-myc inhibition. Authors: Crichlow, G.V. / Zhou, H. / Hsiao, H.H. / Frederick, K.B. / Debrosse, M. / Yang, Y. / Folta-Stogniew, E.J. / Chung, H.J. / Fan, C. / De la Cruz, E.M. / Levens, D. / Lolis, E. / Braddock, D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98.4 KB | Display | ![]() |
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PDB format | ![]() | 70.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.7 KB | Display | ![]() |
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Full document | ![]() | 453.1 KB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kvyC ![]() 5kw1C ![]() 5kwqC ![]() 2qfjS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | Authors have supported the biological unit analysis by performing size exclusion chromatography and light scattering |
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Components
#1: Protein | Mass: 23408.537 Da / Num. of mol.: 2 / Fragment: unp residues 118-316 / Mutation: R123G, C129S, C255A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: DNA chain | | Mass: 8862.427 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: modified adenovirus major late promoter 3' splice site analog Source: (synth.) ![]() #3: Water | ChemComp-HOH / | Sequence details | Guanine 18 in chain C is brominated on carbon C8. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.69 Å3/Da / Density % sol: 27.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 0.1 M Tris-HCl, 25% PEG 4000, 5-10 mM barium chloride dihydrate, pH 8.7, mixed with 10 mg/ml protein-nucleic acid mixture in 50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 20 micromolar EDTA |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 24, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9769 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 28004 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.144 / Net I/av σ(I): 9.34 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.526 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2QFJ Resolution: 1.91→29.29 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED. Data set was de-twinned prior to refinement. Deposited structure factors are the de-twinned ones.
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Solvent computation | Bsol: 45.239 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.91→29.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
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Xplor file |
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