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Yorodumi- PDB-5uwo: Crystal Structure of Engineered FMRP-1b NES Peptide in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uwo | ||||||||||||||||||||||||
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Title | Crystal Structure of Engineered FMRP-1b NES Peptide in complex with CRM1-Ran-RanBP1 | ||||||||||||||||||||||||
Components |
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Keywords | PROTEIN TRANSPORT / HEAT repeat / NES / nuclear export / Karyopherin | ||||||||||||||||||||||||
Function / homology | Function and homology information regulation of translation at presynapse, modulating synaptic transmission / positive regulation of intracellular transport of viral material / modulation by host of viral RNA genome replication / regulation of neuronal action potential / growth cone filopodium / poly(G) binding / positive regulation of miRNA-mediated gene silencing / negative regulation of miRNA-mediated gene silencing / negative regulation of long-term synaptic depression / neuronal ribonucleoprotein granule ...regulation of translation at presynapse, modulating synaptic transmission / positive regulation of intracellular transport of viral material / modulation by host of viral RNA genome replication / regulation of neuronal action potential / growth cone filopodium / poly(G) binding / positive regulation of miRNA-mediated gene silencing / negative regulation of miRNA-mediated gene silencing / negative regulation of long-term synaptic depression / neuronal ribonucleoprotein granule / animal organ development / positive regulation of mitotic centrosome separation / negative regulation of voltage-gated calcium channel activity / dendritic filopodium / RNA strand annealing activity / chromocenter / regulation of dendritic spine development / positive regulation of long-term neuronal synaptic plasticity / MAPK6/MAPK4 signaling / Transport of Mature mRNA derived from an Intron-Containing Transcript / regulation of neurotransmitter secretion / filopodium tip / RNA nuclear export complex / Regulation of HSF1-mediated heat shock response / pre-miRNA export from nucleus / nuclear export signal receptor activity / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / regulation of filopodium assembly / manchette / negative regulation of synaptic vesicle exocytosis / non-membrane-bounded organelle assembly / SUMOylation of SUMOylation proteins / Regulation of cholesterol biosynthesis by SREBP (SREBF) / positive regulation of proteasomal protein catabolic process / importin-alpha family protein binding / N6-methyladenosine-containing RNA reader activity / poly(A) binding / siRNA binding / SUMOylation of RNA binding proteins / regulatory ncRNA-mediated gene silencing / spindle pole body / protein localization to kinetochore / protein localization to nucleolus / glutamate receptor signaling pathway / U4 snRNA binding / Rev-mediated nuclear export of HIV RNA / sequence-specific mRNA binding / nuclear export / Nuclear import of Rev protein / GTP metabolic process / NEP/NS2 Interacts with the Cellular Export Machinery / poly(U) RNA binding / RNA export from nucleus / tRNA processing in the nucleus / SUMOylation of chromatin organization proteins / Postmitotic nuclear pore complex (NPC) reformation / miRNA binding / MicroRNA (miRNA) biogenesis / positive regulation of filopodium assembly / nuclear import signal receptor activity / dynein intermediate chain binding / DNA metabolic process / NLS-bearing protein import into nucleus / dynein complex binding / positive regulation of dendritic spine development / dendritic spine neck / intracellular non-membrane-bounded organelle / regulation of alternative mRNA splicing, via spliceosome / mitotic sister chromatid segregation / glial cell projection / positive regulation of receptor internalization / chromosome, centromeric region / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / mRNA transport / U5 snRNA binding / ribosomal small subunit export from nucleus / ribosomal subunit export from nucleus / translation regulator activity / negative regulation of cytoplasmic translation / U2 snRNA binding / Cajal body / U6 snRNA binding / mRNA export from nucleus / axon terminus / signaling adaptor activity / stress granule assembly / nuclear pore / RNA stem-loop binding / translation repressor activity / U1 snRNA binding / negative regulation of translational initiation / translation initiation factor binding / regulation of mRNA stability / methylated histone binding / centriole / protein export from nucleus / viral process Similarity search - Function | ||||||||||||||||||||||||
Biological species | Homo sapiens (human) Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.347 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 | 5uwo.cif.gz | 814.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uwo.ent.gz | 678.5 KB | Display | PDB format |
PDBx/mmJSON format | 5uwo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/5uwo ftp://data.pdbj.org/pub/pdb/validation_reports/uw/5uwo | HTTPS FTP |
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-Related structure data
Related structure data | 5uwhC 5uwiC 5uwjC 5uwpC 5uwqC 5uwrC 5uwsC 5uwtC 5uwuC 5uwwC 4hb2S C: citing same article (ref.) S: Starting model for refinement |
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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: 117458.781 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: 2306.596 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FMRP / Plasmid: pMal-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q06787*PLUS |
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-Non-polymers , 4 types, 549 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: 2.64 Å3/Da / Density % sol: 53.35 % |
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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, 12 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: 2.35→50 Å / Num. obs: 74260 / % possible obs: 100 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.039 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.35→2.39 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3658 / CC1/2: 0.444 / Rpim(I) all: 0.571 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4HB2 Resolution: 2.347→40.071 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.45 / 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: 2.347→40.071 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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