+Open data
-Basic information
Entry | Database: PDB / ID: 4c0o | ||||||
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Title | Transportin 3 in complex with phosphorylated ASF/SF2 | ||||||
Components |
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Keywords | TRANSPORT PROTEIN/RNA BINDING PROTEIN / TRANSPORT PROTEIN-RNA BINDING PROTEIN COMPLEX / NUCLEAR IMPORT / HEAT REPEAT / SPLICING FACTOR / RRM DOMAIN / RS DOMAIN | ||||||
Function / homology | Function and homology information DNA topoisomerase binding / protein kinase B binding / annulate lamellae / alternative mRNA splicing, via spliceosome / mRNA splice site recognition / mRNA 3'-end processing / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / nuclear import signal receptor activity / mRNA Splicing - Minor Pathway ...DNA topoisomerase binding / protein kinase B binding / annulate lamellae / alternative mRNA splicing, via spliceosome / mRNA splice site recognition / mRNA 3'-end processing / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / nuclear import signal receptor activity / mRNA Splicing - Minor Pathway / regulation of RNA splicing / oligodendrocyte differentiation / Processing of Capped Intron-Containing Pre-mRNA / mRNA 5'-splice site recognition / mRNA transport / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / liver regeneration / mRNA splicing, via spliceosome / mRNA processing / small GTPase binding / protein import into nucleus / nuclear envelope / nuclear speck / mRNA binding / intracellular membrane-bounded organelle / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.557 Å | ||||||
Authors | Maertens, G.N. / Cook, N.J. / Cherepanov, P. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Structural Basis for Nuclear Import of Splicing Factors by Human Transportin 3. Authors: Maertens, G.N. / Cook, N.J. / Wang, W. / Hare, S. / Gupta, S.S. / Oztop, I. / Lee, K. / Pye, V.E. / Cosnefroy, O. / Snijders, A.P. / Kewalramani, V.N. / Fassati, A. / Engelman, A. / Cherepanov, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c0o.cif.gz | 395.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c0o.ent.gz | 322.7 KB | Display | PDB format |
PDBx/mmJSON format | 4c0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/4c0o ftp://data.pdbj.org/pub/pdb/validation_reports/c0/4c0o | HTTPS FTP |
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-Related structure data
Related structure data | 4c0pSC 4c0qC 3begS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper:
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-Components
#1: Protein | Mass: 104313.211 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETSUMO-TNPO3(C511A) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 LAC I / References: UniProt: Q9Y5L0 #2: Protein | Mass: 14555.848 Da / Num. of mol.: 2 Fragment: RESIDUES 106-230 (SECOND RRM DOMAIN AND RS DOMAIN) Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETSUMO-SFRS1(106-230) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS / References: UniProt: Q07955 #3: Chemical | ChemComp-K / | #4: Water | ChemComp-HOH / | Sequence details | FRAGMENT 106-230 | |
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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: 2.77 Å3/Da / Density % sol: 55.7 % / Description: NONE |
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Crystal grow | pH: 6 Details: 16% (W/V) PEG3350, 0.1 M KSCN, 0.1 M BIS-TRIS PROPANE, PH6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.973 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.973 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→47.3 Å / Num. obs: 80114 / % possible obs: 99.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 73.42 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.57→2.71 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.6 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 3BEG AND 4C0P Resolution: 2.557→38.283 Å / SU ML: 0.44 / σ(F): 1.96 / Phase error: 32.67 / 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 mean: 64.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.557→38.283 Å
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Refine LS restraints |
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LS refinement shell |
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