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- PDB-5uwr: Crystal Structure of CDC7 NES Peptide (extended) in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5uwr | ||||||||||||||||||||||||
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Title | Crystal Structure of CDC7 NES Peptide (extended) in complex with CRM1-Ran-RanBP1 | ||||||||||||||||||||||||
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![]() | PROTEIN TRANSPORT / HEAT repeat / NES / nuclear export / Karyopherin | ||||||||||||||||||||||||
Function / homology | ![]() positive regulation of nuclear cell cycle DNA replication / mitotic DNA damage checkpoint signaling / positive regulation of mitotic centrosome separation / cell cycle phase transition / RNA nuclear export complex / pre-miRNA export from nucleus / nuclear export signal receptor activity / snRNA import into nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / cellular response to mineralocorticoid stimulus ...positive regulation of nuclear cell cycle DNA replication / mitotic DNA damage checkpoint signaling / positive regulation of mitotic centrosome separation / cell cycle phase transition / RNA nuclear export complex / pre-miRNA export from nucleus / nuclear export signal receptor activity / snRNA import into nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / cellular response to mineralocorticoid stimulus / Regulation of HSF1-mediated heat shock response / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / SUMOylation of SUMOylation proteins / importin-alpha family protein binding / spindle pole body / protein localization to kinetochore / SUMOylation of RNA binding proteins / protein localization to nucleolus / U4 snRNA binding / Rev-mediated nuclear export of HIV RNA / double-strand break repair via break-induced replication / nuclear export / Nuclear import of Rev protein / GTP metabolic process / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / RNA export from nucleus / SUMOylation of chromatin organization proteins / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / nuclear import signal receptor activity / DNA metabolic process / dynein intermediate chain binding / NLS-bearing protein import into nucleus / intercellular bridge / Transcriptional Regulation by E2F6 / MAPK6/MAPK4 signaling / mitotic sister chromatid segregation / spermatid development / Activation of the pre-replicative complex / ribosomal large subunit export from nucleus / sperm flagellum / U5 snRNA binding / ribosomal small subunit export from nucleus / U2 snRNA binding / U6 snRNA binding / mRNA export from nucleus / Activation of ATR in response to replication stress / ribosomal subunit export from nucleus / nuclear pore / U1 snRNA binding / positive regulation of G2/M transition of mitotic cell cycle / centriole / protein export from nucleus / viral process / GTPase activator activity / 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 / mitotic spindle / kinetochore / small GTPase binding / positive regulation of protein import into nucleus / G1/S transition of mitotic cell cycle / protein import into nucleus / GDP binding / melanosome / positive regulation of protein binding / nuclear envelope / kinase activity / mitotic cell cycle / midbody / actin cytoskeleton organization / ubiquitin-dependent protein catabolic process / non-specific serine/threonine protein kinase / protein kinase activity / cadherin binding / protein heterodimerization activity / protein domain specific binding / phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / GTPase activity / chromatin binding / positive regulation of cell population proliferation / chromatin / nucleolus / GTP binding / perinuclear region of cytoplasm / magnesium ion binding / signal transduction / protein-containing complex / RNA binding / extracellular exosome Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||
![]() | Fung, H.Y.J. / Chook, Y.M. | ||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Nuclear export receptor CRM1 recognizes diverse conformations in nuclear export signals. Authors: Fung, H.Y. / Fu, S.C. / Chook, Y.M. | ||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 818.6 KB | Display | ![]() |
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PDB format | ![]() | 681.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 796.7 KB | Display | ![]() |
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Full document | ![]() | 802 KB | Display | |
Data in XML | ![]() | 50.1 KB | Display | |
Data in CIF | ![]() | 72.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5uwhC ![]() 5uwiC ![]() 5uwjC ![]() 5uwoC ![]() 5uwpC ![]() 5uwqC ![]() 5uwsC ![]() 5uwtC ![]() 5uwuC ![]() 5uwwC ![]() 4hb2S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 26758.564 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 16521.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08 / Plasmid: pGEX-4T3-TEV / Production host: ![]() ![]() |
#3: Protein | Mass: 117458.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: CRM1, KAP124, XPO1, YGR218W, G8514 / Plasmid: pGex-4T3-TEV / Production host: ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules D
#4: Protein/peptide | Mass: 3019.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 528 molecules ![](data/chem/img/GNP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-GNP / | ||||
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#6: Chemical | ChemComp-MG / | ||||
#7: Chemical | #8: Chemical | ChemComp-CL / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.84 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 17% PEG3350, 100 mM Bis-Tris, pH 6.4, 200 mM ammonium nitrate, 10 mM spermine-HCl |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→50 Å / Num. obs: 84118 / % possible obs: 99.4 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.033 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 2.24→2.28 Å / Redundancy: 12 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 4085 / Num. unique obs: 4085 / CC1/2: 0.384 / Rpim(I) all: 0.503 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4HB2 Resolution: 2.24→47.443 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.53 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→47.443 Å
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Refine LS restraints |
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LS refinement shell |
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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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