[English] 日本語
Yorodumi
- PDB-6x2s: Crystal Structure of Mek1(NQ)NES peptide bound to CRM -

+
Open data


ID or keywords:

Loading...

-
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-1Karyopherin
  • 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


MAPK6/MAPK4 signaling / epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / RNA nuclear export complex / nuclear export signal receptor activity / pre-miRNA export from nucleus / snRNA import into nucleus / placenta blood vessel development / cellular response to mineralocorticoid stimulus / manchette ...MAPK6/MAPK4 signaling / epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / RNA nuclear export complex / nuclear export signal receptor activity / pre-miRNA export from nucleus / snRNA import into nucleus / placenta blood vessel development / cellular response to mineralocorticoid stimulus / manchette / regulation of axon regeneration / mitogen-activated protein kinase kinase / type B pancreatic cell proliferation / labyrinthine layer development / MAP-kinase scaffold activity / Regulation of cholesterol biosynthesis by SREBP (SREBF) / cerebellar cortex formation / importin-alpha family protein binding / U4 snRNA binding / Signaling by MAP2K mutants / RNA export from nucleus / spindle pole body / protein localization to kinetochore / nuclear export / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / GTP metabolic process / regulation of Golgi inheritance / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / trachea formation / nuclear import signal receptor activity / regulation of early endosome to late endosome transport / DNA metabolic process / Negative feedback regulation of MAPK pathway / NLS-bearing protein import into nucleus / regulation of stress-activated MAPK cascade / dynein intermediate chain binding / positive regulation of axonogenesis / Frs2-mediated activation / protein kinase activator activity / ERBB2-ERBB3 signaling pathway / ribosomal subunit export from nucleus / face development / endodermal cell differentiation / MAPK3 (ERK1) activation / spermatid development / mitotic sister chromatid segregation / ribosomal small subunit export from nucleus / Bergmann glial cell differentiation / MAP kinase kinase activity / thyroid gland development / Uptake and function of anthrax toxins / ribosomal large subunit export from nucleus / U5 snRNA binding / sperm flagellum / U2 snRNA binding / U6 snRNA binding / mRNA export from nucleus / Schwann cell development / nuclear pore / U1 snRNA binding / keratinocyte differentiation / ERK1 and ERK2 cascade / myelination / protein export from nucleus / centriole / viral process / protein serine/threonine/tyrosine kinase activity / GTPase activator activity / protein serine/threonine kinase activator activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / mitotic spindle organization / G protein activity / insulin-like growth factor receptor signaling pathway / thymus development / Signal transduction by L1 / male germ cell nucleus / cell motility / hippocampus development / Transcriptional regulation by small RNAs / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / G1/S transition of mitotic cell cycle / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / positive regulation of protein serine/threonine kinase activity / neuron differentiation / kinetochore / recycling endosome / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF
Similarity search - Function
Ran-specific GTPase-activating protein 1, Ran-binding domain / Exportin-1, C-terminal / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / CRM1 C terminal / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal ...Ran-specific GTPase-activating protein 1, Ran-binding domain / Exportin-1, C-terminal / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / CRM1 C terminal / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / 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 profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / 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 / P-loop containing nucleotide triphosphate hydrolases / Roll / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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 / Karyopherin / 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

-
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

-
Non-polymers , 4 types, 346 molecules

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


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 / Glycerol


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


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

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more