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Yorodumi- PDB-5uwh: Crystal Structure of Paxillin NES Peptide in complex with CRM1-Ra... -
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Basic information
| Entry | Database: PDB / ID: 5uwh | ||||||||||||||||||||||||
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| Title | Crystal Structure of Paxillin NES Peptide in complex with CRM1-Ran-RanBP1 | ||||||||||||||||||||||||
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Keywords | PROTEIN TRANSPORT / HEAT repeat / NES / nuclear export / Karyopherin | ||||||||||||||||||||||||
| Function / homology | Function and homology informationRegulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response / nuclear export signal receptor activity ...Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response / nuclear export signal receptor activity / Transcriptional and post-translational regulation of MITF-M expression and activity / manchette / cellular response to mineralocorticoid stimulus / neuropilin binding / vinculin binding / Regulation of cholesterol biosynthesis by SREBP (SREBF) / tRNA export from nucleus / importin-alpha family protein binding / SUMOylation of SUMOylation proteins / protein localization to kinetochore / spindle pole body / Rev-mediated nuclear export of HIV RNA / signal complex assembly / Nuclear import of Rev protein / U4 snRNA binding / nuclear export / SUMOylation of RNA binding proteins / protein localization to nucleolus / NEP/NS2 Interacts with the Cellular Export Machinery / RNA export from nucleus / tRNA processing in the nucleus / GTP metabolic process / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of chromatin organization proteins / nuclear import signal receptor activity / microtubule associated complex / growth hormone receptor signaling pathway / MicroRNA (miRNA) biogenesis / DNA metabolic process / MAPK6/MAPK4 signaling / dynein intermediate chain binding / mitotic sister chromatid segregation / ribosomal large subunit export from nucleus / U5 snRNA binding / spermatid development / Smooth Muscle Contraction / viral process / GAB1 signalosome / U2 snRNA binding / U6 snRNA binding / positive regulation of protein binding / endothelial cell migration / sperm flagellum / nuclear pore / mRNA export from nucleus / U1 snRNA binding / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / ribosomal subunit export from nucleus / stress fiber / ribosomal small subunit export from nucleus / positive regulation of stress fiber assembly / centriole / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / GTPase activator activity / protein export from nucleus / mitotic spindle organization / cellular response to reactive oxygen species / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / G1/S transition of mitotic cell cycle / recycling endosome / beta-catenin binding / kinetochore / positive regulation of protein import into nucleus / small GTPase binding / VEGFA-VEGFR2 Pathway / protein import into nucleus / cell-cell junction / GDP binding / melanosome / nuclear envelope / cell migration / mitotic cell cycle / lamellipodium / G protein activity / actin cytoskeleton organization / ubiquitin-dependent protein catabolic process / midbody / cell cortex / protein phosphatase binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cell adhesion / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / focal adhesion / GTPase activity Similarity search - Function | ||||||||||||||||||||||||
| Biological species | Homo sapiens (human)![]() | ||||||||||||||||||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å | ||||||||||||||||||||||||
Authors | Fung, H.Y.J. / Chook, Y.M. | ||||||||||||||||||||||||
| Funding support | United States, Hong Kong, 7items
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Citation | Journal: Elife / Year: 2017Title: 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: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 5uwh.cif.gz | 825.8 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb5uwh.ent.gz | 688.5 KB | Display | PDB format |
| PDBx/mmJSON format | 5uwh.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 5uwh_validation.pdf.gz | 793.9 KB | Display | wwPDB validaton report |
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| Full document | 5uwh_full_validation.pdf.gz | 801 KB | Display | |
| Data in XML | 5uwh_validation.xml.gz | 50.2 KB | Display | |
| Data in CIF | 5uwh_validation.cif.gz | 72.8 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/5uwh ftp://data.pdbj.org/pub/pdb/validation_reports/uw/5uwh | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 5uwiC ![]() 5uwjC ![]() 5uwoC ![]() 5uwpC ![]() 5uwqC ![]() 5uwrC ![]() 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 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: ![]() |
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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: 2497.800 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PXN / Plasmid: pMAL-TEV / Production host: ![]() |
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-Non-polymers , 4 types, 500 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: 2.66 Å3/Da / Density % sol: 53.83 % |
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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, 20 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: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2015 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
| Reflection | Resolution: 2.26→50 Å / Num. obs: 77349 / % possible obs: 91.8 % / Redundancy: 7.3 % / Biso Wilson estimate: 29.8919033835 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.031 / Net I/σ(I): 22.8 |
| Reflection shell | Resolution: 2.26→2.3 Å / Redundancy: 7 % / Num. unique all: 3826 / Num. unique obs: 3826 / CC1/2: 0.621 / Rpim(I) all: 0.461 / % possible all: 92.7 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: PDB entry 4HB2 Resolution: 2.26→47.266 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.72
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| Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 2.26→47.266 Å
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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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Movie
Controller
About Yorodumi



Homo sapiens (human)
X-RAY DIFFRACTION
United States,
Hong Kong, 7items
Citation






















PDBj




















