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- PDB-6x2y: Crystal Structure of mDia2NES peptide bound to CRM1(E571K) -

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Basic information

Entry
Database: PDB / ID: 6x2y
TitleCrystal Structure of mDia2NES peptide bound to CRM1(E571K)
Components
  • Exportin-1
  • GTP-binding nuclear protein Ran
  • Protein diaphanous homolog 3
  • Ran-specific GTPase-activating protein 1
KeywordsPROTEIN TRANSPORT / Nuclear export / CRM1 / XPO1 / Exportin-1
Function / homology
Function and homology information


protein-containing complex remodeling / stereocilia tip-link density / inner ear receptor cell differentiation / ESCRT I complex / actin nucleation / head development / erythrocyte enucleation / actin crosslink formation / podosome assembly / autophagosome-lysosome fusion ...protein-containing complex remodeling / stereocilia tip-link density / inner ear receptor cell differentiation / ESCRT I complex / actin nucleation / head development / erythrocyte enucleation / actin crosslink formation / podosome assembly / autophagosome-lysosome fusion / tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / pre-miRNA export from nucleus / RNA nuclear export complex / ribbon synapse / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response / nuclear export signal receptor activity / Transcriptional and post-translational regulation of MITF-M expression and activity / manchette / cellular response to mineralocorticoid stimulus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / negative regulation of microtubule depolymerization / tRNA export from nucleus / importin-alpha family protein binding / SUMOylation of SUMOylation proteins / protein localization to kinetochore / cell projection organization / spindle pole body / Rev-mediated nuclear export of HIV RNA / RHOD GTPase cycle / Nuclear import of Rev protein / U4 snRNA binding / nuclear export / SUMOylation of RNA binding proteins / protein localization to nucleolus / NEP/NS2 Interacts with the Cellular Export Machinery / RHOF GTPase cycle / RNA export from nucleus / tRNA processing in the nucleus / GTP metabolic process / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of chromatin organization proteins / nuclear import signal receptor activity / endosomal transport / MicroRNA (miRNA) biogenesis / RHOB GTPase cycle / DNA metabolic process / RHOC GTPase cycle / MAPK6/MAPK4 signaling / actin filament bundle / RHOJ GTPase cycle / establishment of cell polarity / filamentous actin / RHOQ GTPase cycle / dynein intermediate chain binding / microtubule polymerization / cleavage furrow / microtubule organizing center / mitotic sister chromatid segregation / CDC42 GTPase cycle / actin filament bundle assembly / macrophage differentiation / ribosomal large subunit export from nucleus / RHOG GTPase cycle / U5 snRNA binding / RHOA GTPase cycle / spermatid development / RAC2 GTPase cycle / RAC3 GTPase cycle / viral process / U2 snRNA binding / U6 snRNA binding / positive regulation of protein binding / sperm flagellum / nuclear pore / mRNA export from nucleus / U1 snRNA binding / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / actin filament polymerization / RAC1 GTPase cycle / cytoskeleton organization / centriole / protein export from nucleus / GTPase activator activity / mitotic spindle organization / integrin-mediated signaling pathway / male germ cell nucleus / actin filament / chromosome segregation / hippocampus development / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / sensory perception of sound / G1/S transition of mitotic cell cycle / recycling endosome / kinetochore / positive regulation of protein import into nucleus / small GTPase binding
Similarity search - Function
Diaphanous, GTPase-binding domain superfamily / : / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain ...Diaphanous, GTPase-binding domain superfamily / : / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain profile. / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 Domain / 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 / Ran GTPase / Small GTPase Ran-type domain profile. / 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 / Protein diaphanous homolog 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.304 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 21, 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_atoms / 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: Protein diaphanous homolog 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,33110
Polymers159,4464
Non-polymers8856
Water8,395466
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11060 Å2
ΔGint-47 kcal/mol
Surface area56610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.666, 106.666, 304.022
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: 117442.875 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

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Protein/peptide , 1 types, 1 molecules D

#4: Protein/peptide Protein diaphanous homolog 3 / Diaphanous-related formin-3 / DRF3 / MDia2


Mass: 1226.512 Da / Num. of mol.: 1 / Fragment: residues 1183-1193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DIAPH3, DIAP3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NSV4

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Non-polymers , 5 types, 472 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 54.63 %
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: Jan 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 113739 / % possible obs: 100 % / Redundancy: 20.6 % / Rmerge(I) obs: 0.319 / Rpim(I) all: 0.071 / Rrim(I) all: 0.327 / Χ2: 0.975 / Net I/σ(I): 3.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.34193.71338590.5610.8613.8130.912100
2.34-2.3819.53.23338670.4480.7393.3180.91100
2.38-2.4319.62.91238650.7180.6642.9880.912100
2.43-2.4819.72.49238690.7680.5682.5570.911100
2.48-2.5319.72.16338670.8140.4922.2190.925100
2.53-2.5919.72.03738670.8730.4632.0890.921100
2.59-2.6619.71.88638410.8970.431.9350.915100
2.66-2.7319.61.6738880.9150.3831.7140.936100
2.73-2.8118.41.52538740.9360.3651.5690.943100
2.81-2.9221.41638940.9690.3041.4490.945100
2.9-322.51.21338760.9770.2571.240.958100
3-3.1222.40.96339020.9860.2050.9850.972100
3.12-3.2622.20.73339110.9910.1570.750.995100
3.26-3.4421.90.52539390.9940.1130.5371.01599.9
3.44-3.6519.80.36439120.9950.0840.3741.066100
3.65-3.9322.50.26739460.9970.0570.2731.12100
3.93-4.3322.60.18339530.9980.0390.1871.127100
4.33-4.9521.70.13240100.9980.0290.1351.093100
4.95-6.2420.40.12840780.9980.0290.1310.931100
6.24-50200.06443110.9990.0150.0660.92899.9

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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: 2.304→45.769 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2563 3040 2.67 %
Rwork0.204 110699 -
obs0.2054 113739 76.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.39 Å2 / Biso mean: 38.671 Å2 / Biso min: 8.95 Å2
Refinement stepCycle: final / Resolution: 2.304→45.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10757 0 4 466 11227
Biso mean--40.58 36.81 -
Num. residues----1333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311112
X-RAY DIFFRACTIONf_angle_d0.51915048
X-RAY DIFFRACTIONf_chiral_restr0.0391716
X-RAY DIFFRACTIONf_plane_restr0.0031909
X-RAY DIFFRACTIONf_dihedral_angle_d14.9396751
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.304-2.340.4657390.334140421
2.34-2.37840.3736640.3158234636
2.3784-2.41940.3319840.2912304946
2.4194-2.46340.3121910.2851331551
2.4634-2.51070.3698930.284338452
2.5107-2.5620.2901980.274347053
2.562-2.61770.2992990.2642356255
2.6177-2.67860.28821120.2529381958
2.6786-2.74560.30381130.2494417263
2.7456-2.81980.27211180.2452450169
2.8198-2.90270.22711530.2468578288
2.9027-2.99640.31771730.244640898
2.9964-3.10350.28731810.2326548100
3.1035-3.22770.25441820.22366574100
3.2277-3.37460.28471730.21496515100
3.3746-3.55240.311780.20846587100
3.5524-3.77490.23071820.18826538100
3.7749-4.06620.22111820.17426573100
4.0662-4.47510.22941830.16366537100
4.4751-5.12190.22621780.15946534100
5.1219-6.45020.27341810.19056555100
6.4502-45.7690.19361830.1683652699

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