+Open data
-Basic information
Entry | Database: PDB / ID: 3fex | ||||||
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Title | Crystal structure of the CBC-importin alpha complex. | ||||||
Components |
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Keywords | TRANSLATION / PROTEIN TRANSPORT / Cap binding complex / importin alpha / nuclear transport / Coiled coil / mRNA transport / Nucleus / Phosphoprotein / RNA-binding / Acetylation / Cytoplasm / Host-virus interaction | ||||||
Function / homology | Function and homology information positive regulation of RNA binding / snRNA export from nucleus / nuclear cap binding complex / mRNA metabolic process / RNA cap binding complex / histone mRNA metabolic process / positive regulation of mRNA 3'-end processing / positive regulation of RNA export from nucleus / Sensing of DNA Double Strand Breaks / regulation of DNA recombination ...positive regulation of RNA binding / snRNA export from nucleus / nuclear cap binding complex / mRNA metabolic process / RNA cap binding complex / histone mRNA metabolic process / positive regulation of mRNA 3'-end processing / positive regulation of RNA export from nucleus / Sensing of DNA Double Strand Breaks / regulation of DNA recombination / cap-dependent translational initiation / Processing of Intronless Pre-mRNAs / snRNA binding / RNA cap binding / alternative mRNA splicing, via spliceosome / entry of viral genome into host nucleus through nuclear pore complex via importin / miRNA-mediated post-transcriptional gene silencing / primary miRNA processing / regulation of mRNA processing / SLBP independent Processing of Histone Pre-mRNAs / positive regulation of viral life cycle / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / regulatory ncRNA-mediated post-transcriptional gene silencing / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / RNA 7-methylguanosine cap binding / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA 3'-end processing / mRNA 3'-end processing / RNA catabolic process / mRNA cis splicing, via spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / Abortive elongation of HIV-1 transcript in the absence of Tat / positive regulation of mRNA splicing, via spliceosome / regulation of translational initiation / FGFR2 alternative splicing / RNA Polymerase II Transcription Termination / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / nuclear import signal receptor activity / DNA metabolic process / CaMK IV-mediated phosphorylation of CREB / Signaling by FGFR2 IIIa TM / nuclear localization sequence binding / NLS-bearing protein import into nucleus / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA polymerase II transcribes snRNA genes / 7-methylguanosine mRNA capping / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / positive regulation of type I interferon production / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / positive regulation of transcription elongation by RNA polymerase II / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / RNA splicing / mRNA transcription by RNA polymerase II / ISG15 antiviral mechanism / histone deacetylase binding / Regulation of expression of SLITs and ROBOs / mRNA splicing, via spliceosome / protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / host cell / positive regulation of cell growth / snRNP Assembly / nuclear membrane / defense response to virus / Estrogen-dependent gene expression / molecular adaptor activity / ribonucleoprotein complex / Golgi membrane / mRNA binding / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / mitochondrion / DNA binding / RNA binding / nucleoplasm / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.549 Å | ||||||
Authors | Dias, S.M.G. / Ambrosio, A.L.B. / Cerione, R.A. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2009 Title: The molecular basis for the regulation of the cap-binding complex by the importins. Authors: Dias, S.M. / Wilson, K.F. / Rojas, K.S. / Ambrosio, A.L. / Cerione, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fex.cif.gz | 233.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fex.ent.gz | 186.6 KB | Display | PDB format |
PDBx/mmJSON format | 3fex.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fex_validation.pdf.gz | 446.7 KB | Display | wwPDB validaton report |
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Full document | 3fex_full_validation.pdf.gz | 465.1 KB | Display | |
Data in XML | 3fex_validation.xml.gz | 43.9 KB | Display | |
Data in CIF | 3fex_validation.cif.gz | 58.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/3fex ftp://data.pdbj.org/pub/pdb/validation_reports/fe/3fex | HTTPS FTP |
-Related structure data
Related structure data | 3feySC 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 91960.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CBP80, NCBP, NCBP1 / Plasmid: pVL1393 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF21 / References: UniProt: Q09161 |
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#2: Protein | Mass: 18028.131 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CBP20, NCBP2, PIG55 / Plasmid: pVL1393 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF21 / References: UniProt: P52298 |
#3: Protein | Mass: 50779.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KPNA2, RCH1, SRP1 / Plasmid: PET 30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52292 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.55 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM KCl, 12% PEG 8000, 100 mM Tris-HCl pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 4, 2007 / Details: Mirror |
Radiation | Monochromator: Horizontal bHorizontal bent Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9179 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→15.652 Å / Num. all: 19814 / Num. obs: 18110 / % possible obs: 91.4 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 74.05 Å2 / Rmerge(I) obs: 0.161 / Rsym value: 0.161 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 3.5→3.62 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 2.58 / Rsym value: 0.428 / % possible all: 92.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FEY Resolution: 3.549→15.652 Å / SU ML: 0.54 / Isotropic thermal model: Group ADP / σ(F): 1.34 / Phase error: 30.56 / 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 / Bsol: 22.202 Å2 / ksol: 0.252 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.549→15.652 Å
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Refine LS restraints |
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LS refinement shell |
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