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- PDB-3nby: Crystal structure of the PKI NES-CRM1-RanGTP nuclear export complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 3nby | ||||||
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Title | Crystal structure of the PKI NES-CRM1-RanGTP nuclear export complex | ||||||
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![]() | GTP-binding protein/transport protein / protein transport / GTP-binding protein-transport protein complex | ||||||
Function / homology | ![]() Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Cyclin A/B1/B2 associated events during G2/M transition / Heme signaling / HuR (ELAVL1) binds and stabilizes mRNA / RNA import into nucleus / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Deactivation of the beta-catenin transactivating complex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion ...Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Cyclin A/B1/B2 associated events during G2/M transition / Heme signaling / HuR (ELAVL1) binds and stabilizes mRNA / RNA import into nucleus / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Deactivation of the beta-catenin transactivating complex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / annulate lamellae / regulation of proteasomal ubiquitin-dependent protein catabolic process / RHO GTPases Activate Formins / Separation of Sister Chromatids / RNA cap binding / regulation of centrosome duplication / RNA nuclear export complex / MAPK6/MAPK4 signaling / pre-miRNA export from nucleus / nuclear export signal receptor activity / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / NLS-dependent protein nuclear import complex / regulation of protein export from nucleus / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / GTP metabolic process / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / nuclear import signal receptor activity / DNA metabolic process / dynein intermediate chain binding / regulation of protein catabolic process / mitotic sister chromatid segregation / protein localization to nucleus / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / ribosomal small subunit export from nucleus / mRNA export from nucleus / ribosomal subunit export from nucleus / nuclear pore / Cajal body / centriole / protein export from nucleus / viral process / mitotic spindle organization / G protein activity / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / recycling endosome / kinetochore / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / snRNP Assembly / midbody / actin cytoskeleton organization / nuclear membrane / DNA-binding transcription factor binding / ribonucleoprotein complex / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / chromatin binding / chromatin / nucleolus / GTP binding / negative regulation of transcription by RNA polymerase II / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guttler, T. / Madl, T. / Neumann, P. / Deichsel, D. / Corsini, L. / Monecke, T. / Ficner, R. / Sattler, M. / Gorlich, D. | ||||||
![]() | ![]() Title: NES consensus redefined by structures of PKI-type and Rev-type nuclear export signals bound to CRM1. Authors: Guttler, T. / Madl, T. / Neumann, P. / Deichsel, D. / Corsini, L. / Monecke, T. / Ficner, R. / Sattler, M. / Gorlich, 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 | ![]() | 613.8 KB | Display | ![]() |
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PDB format | ![]() | 487.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 124.1 KB | Display | |
Data in CIF | ![]() | 167.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2l1lC ![]() 3nbzC ![]() 3nc0C ![]() 3nc1C ![]() 3gjxS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 41228.621 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: PKIA (GeneID: 5569) SNUPN (GeneID: 10073), RNUT1, SNUPN, SPN1 Production host: ![]() ![]() #2: Protein | Mass: 20192.484 Da / Num. of mol.: 2 / Mutation: Q69L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 123367.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Chemical | #5: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 0.1 M Tris/HCl pH range 8.08-8.30, 10-14% (w/v) PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 18, 2005 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Highest resolution: 3.42 Å / Num. obs: 57482 / % possible obs: 83.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.606 Å2 / Rmerge F obs: 0.267 / Rmerge(I) obs: 0.169 / Rrim(I) all: 0.203 / Net I/σ(I): 5.68 / Num. measured all: 169861 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3GJX Resolution: 3.42→38.632 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.54 / Isotropic thermal model: Overall / σ(F): 2 / Phase error: 32.36 / 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: 9.082 Å2 / ksol: 0.296 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.42→38.632 Å
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Refine LS restraints |
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LS refinement shell |
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