+Open data
-Basic information
Entry | Database: PDB / ID: 6x2x | |||||||||
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Title | Crystal Structure of Mek1NES peptide bound to CRM1(E571K) | |||||||||
Components |
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Keywords | PROTEIN TRANSPORT / Nuclear export / CRM1 / XPO1 / Exportin-1 | |||||||||
Function / homology | Function and homology information Transcriptional and post-translational regulation of MITF-M expression and activity / epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / tRNA re-export from nucleus / 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 / placenta blood vessel development ...Transcriptional and post-translational regulation of MITF-M expression and activity / epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / tRNA re-export from nucleus / 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 / placenta blood vessel development / cellular response to mineralocorticoid stimulus / Regulation of HSF1-mediated heat shock response / regulation of axon regeneration / manchette / mitogen-activated protein kinase kinase / labyrinthine layer development / MAP-kinase scaffold activity / type B pancreatic cell proliferation / Regulation of cholesterol biosynthesis by SREBP (SREBF) / cerebellar cortex formation / SUMOylation of SUMOylation proteins / importin-alpha family protein binding / tRNA export from nucleus / Signaling by MAP2K mutants / protein localization to kinetochore / SUMOylation of RNA binding proteins / protein localization to nucleolus / U4 snRNA binding / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / nuclear export / GTP metabolic process / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / regulation of Golgi inheritance / SUMOylation of chromatin organization proteins / RNA export from nucleus / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / spindle pole body / nuclear import signal receptor activity / trachea formation / DNA metabolic process / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / dynein intermediate chain binding / regulation of stress-activated MAPK cascade / positive regulation of axonogenesis / NLS-bearing protein import into nucleus / Frs2-mediated activation / ERBB2-ERBB3 signaling pathway / protein kinase activator activity / endodermal cell differentiation / MAPK3 (ERK1) activation / face development / MAPK6/MAPK4 signaling / mitotic sister chromatid segregation / MAP kinase kinase activity / Bergmann glial cell differentiation / thyroid gland development / Uptake and function of anthrax toxins / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / U5 snRNA binding / male germ cell nucleus / ribosomal subunit export from nucleus / U2 snRNA binding / mRNA export from nucleus / U6 snRNA binding / Schwann cell development / nuclear pore / ribosomal small subunit export from nucleus / U1 snRNA binding / keratinocyte differentiation / Signal transduction by L1 / ERK1 and ERK2 cascade / centriole / protein serine/threonine/tyrosine kinase activity / myelination / viral process / protein export from nucleus / GTPase activator activity / protein serine/threonine kinase activator activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / mitotic spindle organization / insulin-like growth factor receptor signaling pathway / G protein activity / thymus development / cell motility / hippocampus development / Transcriptional regulation by small RNAs / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / positive regulation of protein serine/threonine kinase activity / G1/S transition of mitotic cell cycle / recycling endosome / cellular senescence Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.458 Å | |||||||||
Authors | Baumhardt, J.M. | |||||||||
Funding support | 2items
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Citation | Journal: Mol.Biol.Cell / Year: 2020 Title: Recognition of nuclear export signals by CRM1 carrying the oncogenic E571K mutation. Authors: Baumhardt, J.M. / Walker, J.S. / Lee, Y. / Shakya, B. / Brautigam, C.A. / Lapalombella, R. / Grishin, N. / 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 | 6x2x.cif.gz | 303.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x2x.ent.gz | 235.7 KB | Display | PDB format |
PDBx/mmJSON format | 6x2x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x2x_validation.pdf.gz | 557.1 KB | Display | wwPDB validaton report |
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Full document | 6x2x_full_validation.pdf.gz | 570.6 KB | Display | |
Data in XML | 6x2x_validation.xml.gz | 51.7 KB | Display | |
Data in CIF | 6x2x_validation.cif.gz | 74.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/6x2x ftp://data.pdbj.org/pub/pdb/validation_reports/x2/6x2x | HTTPS FTP |
-Related structure data
Related structure data | 6x2mC 6x2oC 6x2pC 6x2rC 6x2sC 6x2uC 6x2vC 6x2wC 6x2yC 4hb2S S: Starting model for refinement 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: 24456.105 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62826 |
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#2: Protein | Mass: 16320.687 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P41920 |
#3: Protein | Mass: 117442.875 Da / Num. of mol.: 1 / Mutation: E582K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CRM1, KAP124, XPO1, YGR218W, G8514 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30822 |
-Protein/peptide , 1 types, 1 molecules D
#4: Protein/peptide | Mass: 1873.105 Da / Num. of mol.: 1 / Fragment: residues 29-44 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K1, MEK1, PRKMK1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q02750, mitogen-activated protein kinase kinase |
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-Non-polymers , 4 types, 481 molecules
#5: Chemical | ChemComp-GNP / | ||
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#6: Chemical | ChemComp-MG / | ||
#7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.48 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop Details: 17% (weight/vol) PEG3350, 100 mM Bis-Tris (pH 6.4), 200 mM ammonium nitrate, and 10 mM Spermine HCl |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: Aug 1, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.45→50 Å / Num. obs: 65125 / % possible obs: 99.3 % / Redundancy: 34.5 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.019 / Rrim(I) all: 0.098 / Χ2: 0.997 / Net I/σ(I): 5.2 / Num. measured all: 2248198 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HB2 Resolution: 2.458→40.207 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.56 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.73 Å2 / Biso mean: 41.8216 Å2 / Biso min: 9.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.458→40.207 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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