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Yorodumi- PDB-5uww: Crystal Structure of DEAF1 Peptide in complex with CRM1 K579A mut... -
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-Basic information
Entry | Database: PDB / ID: 5uww | ||||||||||||||||||||||||
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Title | Crystal Structure of DEAF1 Peptide in complex with CRM1 K579A mutant-Ran-RanBP1 | ||||||||||||||||||||||||
Components |
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Keywords | PROTEIN TRANSPORT / HEAT repeat / NES / nuclear export / Karyopherin | ||||||||||||||||||||||||
Function / homology | Function and homology information regulation of mammary gland epithelial cell proliferation / positive regulation of mitotic centrosome separation / embryonic skeletal system development / 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 ...regulation of mammary gland epithelial cell proliferation / positive regulation of mitotic centrosome separation / embryonic skeletal system development / 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 / 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 / MAPK6/MAPK4 signaling / germ cell development / mitotic sister chromatid segregation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / U5 snRNA binding / anatomical structure morphogenesis / ribosomal small subunit export from nucleus / U2 snRNA binding / U6 snRNA binding / mRNA export from nucleus / ribosomal subunit export from nucleus / nuclear pore / U1 snRNA binding / centriole / protein export from nucleus / viral process / GTPase activator activity / mitotic spindle organization / G protein activity / male germ cell nucleus / neural tube closure / hippocampus development / Transcriptional regulation by small RNAs / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / recycling endosome / kinetochore / fibrillar center / small GTPase binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / 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 / mitotic cell cycle / midbody / actin cytoskeleton organization / ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / negative regulation of DNA-templated transcription / chromatin binding / chromatin / nucleolus / regulation of transcription by RNA polymerase II / GTP binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus Similarity search - Function | ||||||||||||||||||||||||
Biological species | Homo sapiens (human) Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.152 Å | ||||||||||||||||||||||||
Authors | Fung, H.Y.J. / Chook, Y.M. | ||||||||||||||||||||||||
Funding support | United States, Hong Kong, 7items
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Citation | Journal: Elife / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uww.cif.gz | 819 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uww.ent.gz | 680.1 KB | Display | PDB format |
PDBx/mmJSON format | 5uww.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uww_validation.pdf.gz | 807.4 KB | Display | wwPDB validaton report |
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Full document | 5uww_full_validation.pdf.gz | 813.9 KB | Display | |
Data in XML | 5uww_validation.xml.gz | 52.6 KB | Display | |
Data in CIF | 5uww_validation.cif.gz | 77.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/5uww ftp://data.pdbj.org/pub/pdb/validation_reports/uw/5uww | HTTPS FTP |
-Related structure data
Related structure data | 5uwhC 5uwiC 5uwjC 5uwoC 5uwpC 5uwqC 5uwrC 5uwsC 5uwtC 5uwuC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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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.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Plasmid: pET15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62826 |
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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.) Saccharomyces cerevisiae (brewer's yeast) Gene: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08 / Plasmid: pGEX-4T3-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P41920 |
#3: Protein | Mass: 117400.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CRM1, KAP124, XPO1, YGR218W, G8514 / Plasmid: pGex-4T3-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30822 |
-Protein/peptide , 1 types, 1 molecules D
#4: Protein/peptide | Mass: 2340.566 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DEAF1 / Plasmid: pMal-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75398*PLUS |
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-Non-polymers , 4 types, 725 molecules
#5: Chemical | ChemComp-GNP / | ||
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#6: Chemical | ChemComp-MG / | ||
#7: Chemical | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.96 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 16% PEG3350, 100 mM Bis-Tris, pH 6.4, 200 mM ammonium nitrate, 16 mM HCl |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å |
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: 2.15→50 Å / Num. obs: 95096 / % possible obs: 100 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.025 / Net I/σ(I): 32.2 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4653 / CC1/2: 0.526 / Rpim(I) all: 0.543 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2.152→40.241 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.65 / 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: 2.152→40.241 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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