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- PDB-6m60: Plumbagin in complex with CRM1#-Ran-RanBP1 -

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Basic information

Entry
Database: PDB / ID: 6m60
TitlePlumbagin in complex with CRM1#-Ran-RanBP1
Components
  • Exportin-1Karyopherin
  • GTP-binding nuclear protein Ran
  • Ran-specific GTPase-activating protein 1
KeywordsTRANSPORT PROTEIN / Active Ran / Complex / inhibitor
Function / homology
Function and homology information


positive regulation of mitotic centrosome separation / MAPK6/MAPK4 signaling / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA nuclear export complex / Regulation of HSF1-mediated heat shock response / pre-miRNA export from nucleus / nuclear export signal receptor activity / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette ...positive regulation of mitotic centrosome separation / MAPK6/MAPK4 signaling / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA nuclear export complex / Regulation of HSF1-mediated heat shock response / pre-miRNA export from nucleus / nuclear export signal receptor activity / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / SUMOylation of SUMOylation proteins / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / SUMOylation of RNA binding proteins / spindle pole body / protein localization to kinetochore / protein localization to nucleolus / U4 snRNA binding / Rev-mediated nuclear export of HIV RNA / nuclear export / Nuclear import of Rev protein / GTP metabolic process / RNA export from nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / SUMOylation of chromatin organization proteins / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / nuclear import signal receptor activity / dynein intermediate chain binding / DNA metabolic process / NLS-bearing protein import into nucleus / mitotic sister chromatid segregation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / U5 snRNA binding / ribosomal small subunit export from nucleus / ribosomal subunit export from nucleus / U2 snRNA binding / U6 snRNA binding / mRNA export from nucleus / nuclear pore / U1 snRNA binding / centriole / protein export from nucleus / viral process / GTPase activator activity / mitotic spindle organization / G protein activity / male germ cell nucleus / 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 / recycling endosome / kinetochore / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / midbody / actin cytoskeleton organization / ubiquitin-dependent protein catabolic process / 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, 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 / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-F2X / GUANOSINE-5'-TRIPHOSPHATE / NITRATE ION / 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: 2.17 Å
AuthorsSun, Q. / Lei, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81502629 China
CitationJournal: J.Nat.Prod. / Year: 2021
Title: Novel Mechanistic Observations and NES-Binding Groove Features Revealed by the CRM1 Inhibitors Plumbagin and Oridonin.
Authors: Lei, Y. / Li, Y. / Tan, Y. / Qian, Z. / Zhou, Q. / Jia, D. / Sun, Q.
History
DepositionMar 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,22326
Polymers155,9303
Non-polymers2,29323
Water9,530529
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8380 Å2
ΔGint-44 kcal/mol
Surface area56770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.590, 105.590, 305.040
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: 24399.055 Da / Num. of mol.: 1 / Mutation: Q69L, L182A
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 (E. coli) / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08 / Production host: Escherichia coli (E. coli) / References: UniProt: P41920
#3: Protein Exportin-1 / Karyopherin / Chromosome region maintenance protein 1 / Karyopherin-124


Mass: 115210.508 Da / Num. of mol.: 1
Mutation: S27E , Q49E, del377-413, del441-461, D522K, D537G, T539C, V540E, K541Q, S553R, Q561E, A741T, Y1022C
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 / Production host: Escherichia coli (E. coli) / References: UniProt: P30822

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Non-polymers , 8 types, 552 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: 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
#6: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: NO3
#7: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#10: Chemical ChemComp-F2X / (2~{R})-2-methyl-5-oxidanyl-2,3-dihydronaphthalene-1,4-dione


Mass: 190.195 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C11H10O3 / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 529 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.12 M Monosaccharides (20 mM D-Glucose; 20 mM D-Mannose; 20 mM D-Galactose; 20 mM L-Fucose; 20 mM D-Xylose; 20 mM N-Acetyl-D-Glucosamine), 0.1 M buffer system 1 pH 6.5 (sodium HEPES and ...Details: 0.12 M Monosaccharides (20 mM D-Glucose; 20 mM D-Mannose; 20 mM D-Galactose; 20 mM L-Fucose; 20 mM D-Xylose; 20 mM N-Acetyl-D-Glucosamine), 0.1 M buffer system 1 pH 6.5 (sodium HEPES and MOPS), and 50 % Precipitant Mix 2 (40% v/v Ethylene glycol; 20 % w/v PEG 8000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.17→31.72 Å / Num. obs: 92207 / % possible obs: 100 % / Redundancy: 25.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.027 / Rrim(I) all: 0.135 / Net I/σ(I): 16 / Num. measured all: 2328897 / Scaling rejects: 715
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.17-2.2327.22.22118271567180.5850.4322.2631.9100
9.7-31.7219.50.052297811810.9990.0110.05235.797

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HAT

4hat


Resolution: 2.17→31.72 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 11.228 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 4620 5 %RANDOM
Rwork0.181 ---
obs0.1825 87468 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 159.34 Å2 / Biso mean: 61.795 Å2 / Biso min: 36.68 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å20 Å20 Å2
2---1.25 Å20 Å2
3---2.5 Å2
Refinement stepCycle: final / Resolution: 2.17→31.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10696 0 144 529 11369
Biso mean--83.51 66.8 -
Num. residues----1324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01311057
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710390
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.64614954
X-RAY DIFFRACTIONr_angle_other_deg1.3071.57824138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16851323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57323.617564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.326152017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3271551
X-RAY DIFFRACTIONr_chiral_restr0.070.21456
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212101
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022220
LS refinement shellResolution: 2.17→2.226 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 343 -
Rwork0.282 6347 -
all-6690 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.52830.54230.65171.66820.79623.12040.0446-0.0390.14350.1504-0.0189-0.1073-0.26990.3272-0.02570.108-0.03650.00320.04580.00030.0236-4.61257.228-32.426
23.88621.3009-0.90593.169-0.84344.42470.08240.0111-0.0443-0.0726-0.0642-0.1453-0.18020.4884-0.01830.1579-0.128-0.05150.237-0.00690.120417.01760.203-17.492
30.5611-0.1448-0.06430.4686-0.08620.76710.0102-0.01610.04120.0887-0.00860.0348-0.06510.0054-0.00160.1142-0.04580.00020.0589-0.00650.0195-14.93340.265-30.959
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 216
2X-RAY DIFFRACTION2B80 - 200
3X-RAY DIFFRACTION3C0 - 1052

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