[English] 日本語
![](img/lk-miru.gif)
- PDB-5dis: Crystal structure of a CRM1-RanGTP-SPN1 export complex bound to a... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5dis | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of a CRM1-RanGTP-SPN1 export complex bound to a 113 amino acid FG-repeat containing fragment of Nup214 | |||||||||
![]() |
| |||||||||
![]() | TRANSPORT PROTEIN / FG-repeats / Nucleoporin / Nup214 / Exportin | |||||||||
Function / homology | ![]() cytoplasmic side of nuclear pore / RNA import into nucleus / HuR (ELAVL1) binds and stabilizes mRNA / annulate lamellae / regulation of nucleocytoplasmic transport / regulation of proteasomal ubiquitin-dependent protein catabolic process / RNA cap binding / regulation of centrosome duplication / RNA nuclear export complex / pre-miRNA export from nucleus ...cytoplasmic side of nuclear pore / RNA import into nucleus / HuR (ELAVL1) binds and stabilizes mRNA / annulate lamellae / regulation of nucleocytoplasmic transport / regulation of proteasomal ubiquitin-dependent protein catabolic process / RNA cap binding / regulation of centrosome duplication / RNA nuclear export complex / pre-miRNA export from nucleus / nuclear export signal receptor activity / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / Nuclear Pore Complex (NPC) Disassembly / manchette / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Transport of the SLBP independent Mature mRNA / importin-alpha family protein binding / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / SUMOylation of SUMOylation proteins / regulation of protein export from nucleus / Transport of Mature mRNA Derived from an Intronless Transcript / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / Transport of Mature mRNA derived from an Intron-Containing Transcript / GTP metabolic process / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / RNA export from nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / MicroRNA (miRNA) biogenesis / nuclear import signal receptor activity / Viral Messenger RNA Synthesis / nuclear localization sequence binding / DNA metabolic process / dynein intermediate chain binding / detection of maltose stimulus / maltose transport complex / SUMOylation of ubiquitinylation proteins / Maturation of hRSV A proteins / Vpr-mediated nuclear import of PICs / carbohydrate transport / mitotic sister chromatid segregation / SUMOylation of DNA replication proteins / carbohydrate transmembrane transporter activity / protein localization to nucleus / maltose binding / spermatid development / ribosomal large subunit export from nucleus / maltose transport / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / maltodextrin transmembrane transport / Regulation of HSF1-mediated heat shock response / sperm flagellum / ribosomal small subunit export from nucleus / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / ribosomal subunit export from nucleus / nuclear pore / Cyclin A/B1/B2 associated events during G2/M transition / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / Cajal body / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / NPAS4 regulates expression of target genes / centriole / protein export from nucleus / viral process / ATP-binding cassette (ABC) transporter complex / SUMOylation of chromatin organization proteins / Downregulation of TGF-beta receptor signaling / cell chemotaxis / mitotic spindle organization / HCMV Late Events / G protein activity / male germ cell nucleus / Deactivation of the beta-catenin transactivating complex / RHO GTPases Activate Formins / hippocampus development / Transcriptional regulation by small RNAs / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Heme signaling / MAPK6/MAPK4 signaling / recycling endosome / ISG15 antiviral mechanism / kinetochore / small GTPase binding / positive regulation of protein import into nucleus / HCMV Early Events Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Monecke, T. / Port, S.A. / Dickmanns, A. / Kehlenbach, R.H. / Ficner, R. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structural and Functional Characterization of CRM1-Nup214 Interactions Reveals Multiple FG-Binding Sites Involved in Nuclear Export. Authors: Port, S.A. / Monecke, T. / Dickmanns, A. / Spillner, C. / Hofele, R. / Urlaub, H. / Ficner, R. / Kehlenbach, R.H. #1: ![]() Title: Combining dehydration, construct optimization and improved data collection to solve the crystal structure of a CRM1-RanGTP-SPN1-Nup214 quaternary export complex Authors: Monecke, T. / Dickmanns, A. / Weiss, M.S. / Port, S.A. / Kehlenbach, R.H. / Ficner, R. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 788.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 642.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 64.1 KB | Display | |
Data in CIF | ![]() | 86.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 4 types, 4 molecules ABCD
#1: Protein | Mass: 120395.742 Da / Num. of mol.: 1 / Fragment: UNP residues 5-1058 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 19812.088 Da / Num. of mol.: 1 / Fragment: UNP residues 8-179 / Mutation: Q69L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 33276.527 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Protein | Mass: 50577.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: malE, b4034, JW3994, NUP214, CAIN, CAN, KIAA0023 / Production host: ![]() ![]() |
-Sugars , 1 types, 1 molecules
#5: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
---|
-Non-polymers , 4 types, 16 molecules ![](data/chem/img/PRO.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #7: Chemical | ChemComp-GTP / | #8: Chemical | ChemComp-MG / | #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.56 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 5% PEG 8000, 0.2M L-proline, 0.1M Tris pH 7.5, 4 mM D-maltose, 180 mM LiCl |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si111-DCM with sagital bender / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.85→48.49 Å / Num. obs: 67922 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 80.01 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.062 / Χ2: 1.037 / Net I/σ(I): 15.52 / Num. measured all: 313050 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3GJX, 1ANF Resolution: 2.85→48.485 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.17 / Stereochemistry target values: ML Details: Overall, the electron density map for MBP and especially its N-terminal lobe is of poor quality. This suggests that significant movement of MBP in the crystal lattice is possible, which is ...Details: Overall, the electron density map for MBP and especially its N-terminal lobe is of poor quality. This suggests that significant movement of MBP in the crystal lattice is possible, which is consistent with the overall elevated B-factors of the MBP residues. Hence, several parts of MBP are not defined in the electron density map. Since dissolved crystals analysed by SDS-PAGE clearly showed the presence of full-length MBP in order to retain structural integrity of the crystal lattice and the MBP, the residues were not omitted.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→48.485 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|