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- PDB-6x2r: Crystal Structure of the 4E-TNES peptide bound to CRM1 -

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Basic information

Entry
Database: PDB / ID: 6x2r
TitleCrystal Structure of the 4E-TNES peptide bound to CRM1
Components
  • Eukaryotic translation initiation factor 4E transporter
  • 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


negative regulation of deadenylation-dependent decapping of nuclear-transcribed mRNA / 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 / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response / nuclear export signal receptor activity / miRNA-mediated gene silencing by inhibition of translation ...negative regulation of deadenylation-dependent decapping of nuclear-transcribed mRNA / 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 / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response / nuclear export signal receptor activity / miRNA-mediated gene silencing by inhibition of translation / Regulation of cholesterol biosynthesis by SREBP (SREBF) / tRNA export from nucleus / SUMOylation of SUMOylation proteins / protein localization to kinetochore / 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 / mRNA stabilization / nuclear export / NEP/NS2 Interacts with the Cellular Export Machinery / GTP metabolic process / tRNA processing in the nucleus / RNA export from nucleus / P-body assembly / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of chromatin organization proteins / nuclear import signal receptor activity / MicroRNA (miRNA) biogenesis / DNA metabolic process / stem cell population maintenance / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / MAPK6/MAPK4 signaling / mitotic sister chromatid segregation / ribosomal large subunit export from nucleus / negative regulation of neuron differentiation / U5 snRNA binding / viral process / U2 snRNA binding / U6 snRNA binding / nuclear pore / ribosomal subunit export from nucleus / mRNA export from nucleus / U1 snRNA binding / ribosomal small subunit export from nucleus / centriole / GTPase activator activity / protein export from nucleus / mitotic spindle organization / Transcriptional regulation by small RNAs / P-body / PML body / recycling endosome / small GTPase binding / kinetochore / kinase binding / G1/S transition of mitotic cell cycle / positive regulation of protein import into nucleus / neuron differentiation / protein import into nucleus / GDP binding / positive regulation of protein binding / nuclear envelope / melanosome / mitotic cell cycle / G protein activity / midbody / ubiquitin-dependent protein catabolic process / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / negative regulation of translation / nuclear speck / cadherin binding / translation / protein heterodimerization activity / cell division / GTPase activity / intracellular membrane-bounded organelle / mRNA binding / chromatin binding / GTP binding / chromatin / nucleolus / perinuclear region of cytoplasm / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Eukaryotic translation initiation factor 4E binding protein / Nucleocytoplasmic shuttling protein for mRNA cap-binding EIF4E / 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 ...Eukaryotic translation initiation factor 4E binding protein / Nucleocytoplasmic shuttling protein for mRNA cap-binding EIF4E / 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 / 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 / Eukaryotic translation initiation factor 4E transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.299 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: Eukaryotic translation initiation factor 4E transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,6179
Polymers159,7944
Non-polymers8235
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11000 Å2
ΔGint-57 kcal/mol
Surface area56530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.602, 106.602, 303.674
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11C-1261-

HOH

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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 Eukaryotic translation initiation factor 4E transporter / eIF4E transporter / Eukaryotic translation initiation factor 4E nuclear import factor 1


Mass: 1574.771 Da / Num. of mol.: 1 / Fragment: residues 434-448
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4ENIF1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NRA8

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Non-polymers , 4 types, 175 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.: 170 / 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: 2.7 Å3/Da / Density % sol: 54.42 %
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: Mar 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.299→50 Å / Num. obs: 78790 / % possible obs: 99.9 % / Redundancy: 15.8 % / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.04 / Rrim(I) all: 0.165 / Χ2: 0.726 / Net I/σ(I): 4.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.3414.43.31238520.5050.8453.4230.42499.9
2.34-2.3814.32.91438670.5750.7423.0110.42599.9
2.38-2.4313.32.58738830.6530.6952.6820.42699.8
2.43-2.4815.52.2138650.7560.542.2780.43499.8
2.48-2.5315.81.75738760.8250.4221.810.43999.8
2.53-2.5915.81.47938890.8840.3571.5240.44199.9
2.59-2.6615.81.17938680.90.2861.2140.45399.9
2.66-2.7315.60.90238910.9360.2210.930.45399.9
2.73-2.8115.30.70439030.9510.1750.7260.45899.9
2.81-2.915.20.53939030.9690.1360.5570.482100
2.9-314.30.438750.980.1060.4140.5199.9
3-3.1216.50.30139360.9890.0730.310.53100
3.12-3.2616.60.2239260.9930.0540.2260.584100
3.26-3.4416.70.1639360.9950.040.1650.683100
3.44-3.6516.80.12339350.9960.0310.1270.807100
3.65-3.9315.50.10139670.9970.0260.1051.04599.9
3.93-4.33180.08539870.9970.0210.0881.228100
4.33-4.9517.70.07940190.9980.0190.0811.457100
4.95-6.2416.20.07640720.9980.0190.0781.32499.9
6.24-5016.10.05543400.9990.0140.0561.42399.9

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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: 2.299→42.019 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.257 1999 2.54 %
Rwork0.2222 76633 -
obs0.2231 78632 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.97 Å2 / Biso mean: 64.385 Å2 / Biso min: 25.87 Å2
Refinement stepCycle: final / Resolution: 2.299→42.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10764 0 0 170 10934
Biso mean---55.64 -
Num. residues----1337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511133
X-RAY DIFFRACTIONf_angle_d0.69115078
X-RAY DIFFRACTIONf_chiral_restr0.0421719
X-RAY DIFFRACTIONf_plane_restr0.0041914
X-RAY DIFFRACTIONf_dihedral_angle_d5.1639384
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.299-2.35630.36721360.3164527998
2.3563-2.420.38191410.29825369100
2.42-2.49120.29071410.28075398100
2.4912-2.57160.3331390.27595371100
2.5716-2.66350.31761430.26655441100
2.6635-2.77010.28121410.2685401100
2.7701-2.89610.29541420.2625440100
2.8961-3.04880.30651420.26155459100
3.0488-3.23970.29821420.25755449100
3.2397-3.48970.27461430.24795478100
3.4897-3.84070.27281440.21925505100
3.8407-4.3960.23271450.19375539100
4.396-5.53650.22271460.18445627100
5.5365-42.0190.19781540.1875877100

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