+Open data
-Basic information
Entry | Database: PDB / ID: 3gb8 | ||||||
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Title | Crystal structure of CRM1/Snurportin-1 complex | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Nuclear Transport Complex / Host-virus interaction / mRNA transport / Nucleus / Phosphoprotein / Protein transport / RNA-binding / Transport | ||||||
Function / homology | Function and homology information RNA import into nucleus / HuR (ELAVL1) binds and stabilizes mRNA / annulate lamellae / regulation of proteasomal ubiquitin-dependent protein catabolic process / RNA cap binding / regulation of centrosome duplication / nuclear export signal receptor activity / snRNA import into nucleus / NLS-dependent protein nuclear import complex / regulation of protein export from nucleus ...RNA import into nucleus / HuR (ELAVL1) binds and stabilizes mRNA / annulate lamellae / regulation of proteasomal ubiquitin-dependent protein catabolic process / RNA cap binding / regulation of centrosome duplication / nuclear export signal receptor activity / snRNA import into nucleus / NLS-dependent protein nuclear import complex / regulation of protein export from nucleus / Rev-mediated nuclear export of HIV RNA / NEP/NS2 Interacts with the Cellular Export Machinery / nucleocytoplasmic transport / nuclear import signal receptor activity / Cajal body / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Cyclin A/B1/B2 associated events during G2/M transition / Maturation of hRSV A proteins / protein localization to nucleus / ribosomal large subunit export from nucleus / Transcriptional and post-translational regulation of MITF-M expression and activity / ribosomal subunit export from nucleus / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / mRNA export from nucleus / nuclear pore / ribosomal small subunit export from nucleus / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / NPAS4 regulates expression of target genes / protein export from nucleus / Downregulation of TGF-beta receptor signaling / Deactivation of the beta-catenin transactivating complex / RHO GTPases Activate Formins / Heme signaling / MAPK6/MAPK4 signaling / kinetochore / small GTPase binding / protein import into nucleus / Separation of Sister Chromatids / nuclear envelope / ribosome biogenesis / snRNP Assembly / nuclear membrane / ribonucleoprotein complex / intracellular membrane-bounded organelle / nucleolus / protein-containing complex / RNA binding / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å | ||||||
Authors | Dong, X. / Biswas, A. / Suel, K.E. / Jackson, L.K. / Martinez, R. / Gu, H. / Chook, Y.M. | ||||||
Citation | Journal: Nature / Year: 2009 Title: Structural basis for leucine-rich nuclear export signal recognition by CRM1. Authors: Dong, X. / Biswas, A. / Suel, K.E. / Jackson, L.K. / Martinez, R. / Gu, H. / Chook, Y.M. #1: Journal: To be Published / Year: 2009 Title: Structural basis of assembly and disassembly of the CRM1 nuclear export complex Authors: Dong, X. / Biswas, A. / Chook, Y.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gb8.cif.gz | 254.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gb8.ent.gz | 200.7 KB | Display | PDB format |
PDBx/mmJSON format | 3gb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gb8_validation.pdf.gz | 448 KB | Display | wwPDB validaton report |
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Full document | 3gb8_full_validation.pdf.gz | 485.9 KB | Display | |
Data in XML | 3gb8_validation.xml.gz | 44.5 KB | Display | |
Data in CIF | 3gb8_validation.cif.gz | 61 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/3gb8 ftp://data.pdbj.org/pub/pdb/validation_reports/gb/3gb8 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 123518.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRM1, XPO1 / Plasmid: pGEXTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14980 |
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#2: Protein | Mass: 37766.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RNUT1, SNUPN, SPN1 / Plasmid: pGEXTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O95149 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.34 Å3/Da / Density % sol: 76.97 % Description: The structure factor file contains Bijvoet pairs. |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6.5 Details: 8% PEG 8000, 0.2M Magnesium chloride, 0.1M MES pH 6.5, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935, 0.97945, 0.97167 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2008 Details: LN2 cooled first crystal, sagital focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror | ||||||||||||
Radiation | Monochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.9→50 Å / Num. obs: 73476 / % possible obs: 99.1 % / Redundancy: 7.4 % / Rsym value: 0.083 / Net I/σ(I): 25 | ||||||||||||
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.58 / % possible all: 99.6 |
-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.9→47.67 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.877 / Occupancy max: 1 / Occupancy min: 1 / SU B: 24.996 / SU ML: 0.213 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.399 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. The Bijvoet pairs were used in phasing. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.05 Å2 / Biso mean: 44.541 Å2 / Biso min: 4.68 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→47.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.975 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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