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- PDB-5yst: RanM189D in complex with RanBP1-CRM1 -

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Basic information

Entry
Database: PDB / ID: 5yst
TitleRanM189D in complex with RanBP1-CRM1
Components
  • Exportin-1,Exportin-1
  • GTP-binding nuclear protein Ran
  • Ran-specific GTPase-activating protein 1
KeywordsPROTEIN TRANSPORT / transport protein / nuclear export / complex / mutant / activation
Function / homology
Function and homology information


Transcriptional and post-translational regulation of MITF-M expression and activity / tRNA re-export from nucleus / RNA nuclear export complex / pre-miRNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear export signal receptor activity / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response / manchette / cellular response to mineralocorticoid stimulus ...Transcriptional and post-translational regulation of MITF-M expression and activity / tRNA re-export from nucleus / RNA nuclear export complex / pre-miRNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear export signal receptor activity / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response / manchette / cellular response to mineralocorticoid stimulus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / tRNA export from nucleus / SUMOylation of SUMOylation proteins / importin-alpha family protein binding / 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 / RNA export from nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / GTP metabolic process / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of chromatin organization proteins / spindle pole body / MicroRNA (miRNA) biogenesis / nuclear import signal receptor activity / DNA metabolic process / dynein intermediate chain binding / NLS-bearing protein import into nucleus / MAPK6/MAPK4 signaling / mitotic sister chromatid segregation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / U5 snRNA binding / viral process / mRNA export from nucleus / U2 snRNA binding / U6 snRNA binding / nuclear pore / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / U1 snRNA binding / protein export from nucleus / centriole / GTPase activator activity / mitotic spindle organization / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / recycling endosome / G protein activity / kinetochore / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / G1/S transition of mitotic cell cycle / GDP binding / melanosome / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / midbody / actin cytoskeleton organization / ubiquitin-dependent protein catabolic process / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / chromatin binding / chromatin / nucleolus / GTP binding / perinuclear region of cytoplasm / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
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 / CRM1 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 domain / Ran binding protein RanBP1-like / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Exportin-1 / Ran-specific GTPase-activating protein 1 / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsSun, Q. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
NSFC China
CitationJournal: To Be Published
Title: RanM189D in complex with RanBP1-CRM1
Authors: Sun, Q. / Zhang, Y.
History
DepositionNov 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP-binding nuclear protein Ran
B: Ran-specific GTPase-activating protein 1
C: Exportin-1,Exportin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,67918
Polymers157,3723
Non-polymers1,30715
Water11,458636
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11840 Å2
ΔGint-111 kcal/mol
Surface area55990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.884, 104.884, 307.822
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: 24439.998 Da / Num. of mol.: 1 / Mutation: M189D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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: 16249.607 Da / Num. of mol.: 1 / Fragment: Ran Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08 / Plasmid: pGEX4t-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P41920
#3: Protein Exportin-1,Exportin-1 / Chromosome region maintenance protein 1 / Karyopherin-124


Mass: 116682.086 Da / Num. of mol.: 1
Fragment: lacking C-terminal inhibitory tail,lacking C-terminal inhibitory tail
Mutation: D537G, T539C, V540E, K541Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CRM1, KAP124, XPO1, YGR218W, G8514 / Plasmid: pGEX4t-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30822

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Non-polymers , 6 types, 651 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 636 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsNatural mutation at this position

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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: 2.69 Å3/Da / Density % sol: 54.27 % / Mosaicity: 0.905 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 18% PEG 3350, 200mM Ammonium Nitrate, 100mM Bis-Tris pH 6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97921 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 110107 / % possible obs: 100 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.058 / Rrim(I) all: 0.163 / Χ2: 0.811 / Net I/σ(I): 3
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2Rmerge(I) obsRrim(I) all
2.04-2.0813.154170.3030.7660.647
2.08-2.1113.154390.4450.6410.635
2.11-2.151354020.5290.560.637
2.15-2.212.953970.6260.4930.644
2.2-2.2512.754300.6860.4250.659
2.25-2.31254350.7570.3560.677
2.3-2.3512.854400.8250.3010.674
2.35-2.4213.454480.8710.2570.6910.9090.945
2.42-2.4913.454350.9180.2080.7130.7360.765
2.49-2.5713.254690.930.1760.7220.6170.642
2.57-2.661354530.950.1460.7610.5090.53
2.66-2.7712.554700.9670.1190.7890.4050.422
2.77-2.8912.654880.9770.0930.8370.3180.331
2.89-3.0513.554920.9830.0740.8880.2610.271
3.05-3.2413.454990.9880.0580.9360.2050.213
3.24-3.4913.255560.9910.0481.0810.1670.174
3.49-3.8412.655430.9910.0421.0140.1430.149
3.84-4.3913.656150.9920.0371.0470.130.135
4.39-5.5412.656800.9930.0341.0860.1190.124
5.54-5012.459990.9940.0311.0170.1020.107

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HAT

4hat


Resolution: 2.04→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.1943 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.165 / Details: Refmac and Phenix
RfactorNum. reflection% reflectionSelection details
Rfree0.2377 5422 4.9 %RANDOM
Rwork0.2092 ---
obs0.2106 104505 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 147.77 Å2 / Biso mean: 48.912 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å2-0 Å2-0 Å2
2--0.95 Å20 Å2
3----1.91 Å2
Refinement stepCycle: final / Resolution: 2.04→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10876 0 74 636 11586
Biso mean--63.22 50.12 -
Num. residues----1348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01911187
X-RAY DIFFRACTIONr_bond_other_d00.0210539
X-RAY DIFFRACTIONr_angle_refined_deg1.1141.96415147
X-RAY DIFFRACTIONr_angle_other_deg3.414324504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65951356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93725.057524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.529152053
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9781551
X-RAY DIFFRACTIONr_chiral_restr0.0380.21735
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212202
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022197
LS refinement shellResolution: 2.04→2.093 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 397 -
Rwork0.351 7516 -
all-7913 -
obs--98.53 %

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