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- PDB-6x2s: Crystal Structure of Mek1(NQ)NES peptide bound to CRM -

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Basic information

Entry
Database: PDB / ID: 6x2s
TitleCrystal Structure of Mek1(NQ)NES peptide bound to CRM
Components
  • Dual specificity mitogen-activated protein kinase kinase 1
  • Exportin-1
  • GTP-binding nuclear protein Ran
  • Ran-specific GTPase-activating protein 1
KeywordsPROTEIN TRANSPORT / Nuclear export / CRM1 / XPO1 / Exportin-1
Function / homology
Function and homology information


epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / pre-miRNA export from nucleus / RNA nuclear export complex / Transcriptional and post-translational regulation of MITF-M expression and activity / JUN kinase kinase activity / snRNA import into nucleus / regulation of axon regeneration ...epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / pre-miRNA export from nucleus / RNA nuclear export complex / Transcriptional and post-translational regulation of MITF-M expression and activity / JUN kinase kinase activity / snRNA import into nucleus / regulation of axon regeneration / Regulation of HSF1-mediated heat shock response / mitogen-activated protein kinase kinase / nuclear export signal receptor activity / placenta blood vessel development / MAP-kinase scaffold activity / labyrinthine layer development / cerebellar cortex formation / type B pancreatic cell proliferation / Regulation of cholesterol biosynthesis by SREBP (SREBF) / tRNA export from nucleus / SUMOylation of SUMOylation proteins / protein localization to kinetochore / Signaling by MAP2K mutants / SUMOylation of RNA binding proteins / protein localization to nucleolus / U4 snRNA binding / Rev-mediated nuclear export of HIV RNA / spindle pole body / Nuclear import of Rev protein / nuclear export / positive regulation of axonogenesis / NEP/NS2 Interacts with the Cellular Export Machinery / GTP metabolic process / tRNA processing in the nucleus / RNA export from nucleus / Postmitotic nuclear pore complex (NPC) reformation / regulation of Golgi inheritance / SUMOylation of chromatin organization proteins / nuclear import signal receptor activity / MicroRNA (miRNA) biogenesis / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / DNA metabolic process / MAPK3 (ERK1) activation / Frs2-mediated activation / ERBB2-ERBB3 signaling pathway / MAPK6/MAPK4 signaling / endodermal cell differentiation / face development / MAP kinase kinase activity / Bergmann glial cell differentiation / Uptake and function of anthrax toxins / mitotic sister chromatid segregation / thyroid gland development / protein kinase activator activity / ribosomal large subunit export from nucleus / U5 snRNA binding / viral process / positive regulation of protein serine/threonine kinase activity / U2 snRNA binding / U6 snRNA binding / nuclear pore / ribosomal subunit export from nucleus / mRNA export from nucleus / Schwann cell development / U1 snRNA binding / keratinocyte differentiation / ribosomal small subunit export from nucleus / myelination / centriole / ERK1 and ERK2 cascade / protein serine/threonine/tyrosine kinase activity / GTPase activator activity / insulin-like growth factor receptor signaling pathway / protein export from nucleus / protein serine/threonine kinase activator activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / thymus development / mitotic spindle organization / Signal transduction by L1 / cell motility / Transcriptional regulation by small RNAs / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / recycling endosome / small GTPase binding / kinetochore / G1/S transition of mitotic cell cycle / positive regulation of protein import into nucleus / neuron differentiation / protein import into nucleus / chemotaxis / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / GDP binding
Similarity search - Function
Ran-specific GTPase-activating protein 1, Ran-binding domain / : / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1, C-terminal ...Ran-specific GTPase-activating protein 1, Ran-binding domain / : / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1, C-terminal / CRM1 C terminal / Exportin-1/5 / Exportin-1/Importin-beta-like / Exportin 1-like protein / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / small GTPase Ran family profile. / Ran GTPase / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / PH-like domain superfamily / Armadillo-type fold / Roll / P-loop containing nucleotide triphosphate hydrolases / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Exportin-1 / Ran-specific GTPase-activating protein 1 / GTP-binding nuclear protein Ran / Dual specificity mitogen-activated protein kinase kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.496 Å
AuthorsBaumhardt, J.M.
Funding support2items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)
Welch Foundation
CitationJournal: 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
DepositionMay 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTP-binding nuclear protein Ran
B: Ran-specific GTPase-activating protein 1
C: Exportin-1
D: Dual specificity mitogen-activated protein kinase kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,9579
Polymers160,1344
Non-polymers8235
Water6,143341
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.898, 106.898, 303.449
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein GTP-binding nuclear protein Ran / Androgen receptor-associated protein 24 / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear 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
#2: Protein Ran-specific GTPase-activating protein 1 / Chromosome stability protein 20 / Perinuclear array-localized protein / Ran-binding protein 1 / RANBP1


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 Exportin-1 / Chromosome region maintenance protein 1 / Karyopherin-124


Mass: 117442.812 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30822

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Protein/peptide , 1 types, 1 molecules D

#4: Protein/peptide Dual specificity mitogen-activated protein kinase kinase 1 / MKK1 / ERK activator kinase 1 / MAPK/ERK kinase 1 / MEK 1


Mass: 1914.160 Da / Num. of mol.: 1 / Fragment: residues 29-44 / Mutation: D43N, E44Q
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, 346 molecules

#5: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.54 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.496→50 Å / Num. obs: 62200 / % possible obs: 99.9 % / Redundancy: 18.1 % / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.035 / Rrim(I) all: 0.15 / Χ2: 1.003 / Net I/σ(I): 5.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.5415.32.19730450.5910.562.270.92299.8
2.54-2.5916.92.0930120.6620.5072.1530.91699.9
2.59-2.6418.11.74130640.7540.411.790.924100
2.64-2.6918.11.49530710.8060.3531.5370.96100
2.69-2.7518.21.29730750.8320.3061.3340.945100
2.75-2.8218.11.0330530.8730.2441.0590.925100
2.82-2.8918.10.83430610.9270.1980.8580.938100
2.89-2.9617.90.68130650.9470.1630.7010.932100
2.96-3.0517.50.54530750.9640.1320.5610.935100
3.05-3.1516.10.41330880.9750.1040.4260.93999.8
3.15-3.26190.32930530.9880.0770.3380.962100
3.26-3.39190.24631000.9890.0570.2530.981100
3.39-3.5518.90.19130980.9940.0450.1961.04100
3.55-3.7318.80.14830960.9950.0350.1521.081100
3.73-3.9718.30.11631350.9970.0280.121.104100
3.97-4.2717.60.09431220.9970.0230.0961.12999.8
4.27-4.719.70.08231430.9980.0190.0841.208100
4.7-5.3819.20.07731820.9980.0180.0791.169100
5.38-6.7818.10.07332250.9980.0170.0751.00299.8
6.78-5019.30.05134370.9990.0120.0530.9899.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HB2

4hb2


Resolution: 2.496→47.324 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 1999 3.32 %
Rwork0.1961 58221 -
obs0.1978 60220 96.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.35 Å2 / Biso mean: 43.622 Å2 / Biso min: 6.35 Å2
Refinement stepCycle: final / Resolution: 2.496→47.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10835 0 0 341 11176
Biso mean---40.25 -
Num. residues----1343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311177
X-RAY DIFFRACTIONf_angle_d0.58215138
X-RAY DIFFRACTIONf_chiral_restr0.041726
X-RAY DIFFRACTIONf_plane_restr0.0031922
X-RAY DIFFRACTIONf_dihedral_angle_d4.7089421
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4964-2.55880.35811020.2649297371
2.5588-2.6280.29971330.2525388092
2.628-2.70530.32861390.2485403696
2.7053-2.79270.34131430.2427416699
2.7927-2.89250.28021450.23844215100
2.8925-3.00820.31991450.22484215100
3.0082-3.14510.27841470.21694277100
3.1451-3.31090.27851450.21254224100
3.3109-3.51830.24281470.20144280100
3.5183-3.78980.2391470.18584293100
3.7898-4.1710.19961470.16994289100
4.171-4.77410.21361500.15844343100
4.7741-6.01290.24721510.18144399100
6.0129-47.3240.18241580.17254631100

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