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- PDB-9vm1: MVM NS2 mutant Nm42 in complex with CRM1-Ran-RanBP1 -

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Basic information

Entry
Database: PDB / ID: 9vm1
TitleMVM NS2 mutant Nm42 in complex with CRM1-Ran-RanBP1
Components
  • ASP-GLY-TYR-ILE-GLU-GLU-LEU-ILE-ARG-MET-PHE-GLY-LYS-LEU-SER-ILE-HIS-ASP-ASP
  • Exportin-1
  • GTP-binding nuclear protein Ran
  • Ran-specific GTPase-activating protein 1
KeywordsTRANSPORT PROTEIN / nuclear export / complex / mutant / inhibitor
Function / homology
Function and homology information


tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / pre-miRNA export from nucleus / RNA nuclear export complex / 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 ...tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / pre-miRNA export from nucleus / RNA nuclear export complex / 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) / tRNA export from nucleus / importin-alpha family protein binding / SUMOylation of SUMOylation proteins / protein localization to kinetochore / spindle pole body / Rev-mediated nuclear export of HIV RNA / 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 / RNA export from nucleus / GTP metabolic process / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of chromatin organization proteins / nuclear import signal receptor activity / MicroRNA (miRNA) biogenesis / DNA metabolic process / MAPK6/MAPK4 signaling / dynein intermediate chain binding / mitotic sister chromatid segregation / ribosomal large subunit export from nucleus / U5 snRNA binding / spermatid development / viral process / U2 snRNA binding / U6 snRNA binding / positive regulation of protein binding / sperm flagellum / nuclear pore / mRNA export from nucleus / ribosomal subunit export from nucleus / U1 snRNA binding / ribosomal small subunit export from nucleus / centriole / GTPase activator activity / protein export from nucleus / mitotic spindle organization / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / G1/S transition of mitotic cell cycle / recycling endosome / kinetochore / positive regulation of protein import into nucleus / small GTPase binding / protein import into nucleus / GDP binding / melanosome / nuclear envelope / mitotic cell cycle / G protein activity / actin cytoskeleton organization / midbody / 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 / GTP binding / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / nucleus / membrane / cytoplasm / cytosol
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 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 / 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
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 S288C (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSun, Q. / Li, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82273850 China
CitationJournal: Int J Nanomedicine / Year: 2021
Title: Cancer Therapy with Nanoparticle-Medicated Intracellular Expression of Peptide CRM1-Inhibitor.
Authors: Sui, M. / Xiong, M. / Li, Y. / Zhou, Q. / Shen, X. / Jia, D. / Gou, M. / Sun, Q.
History
DepositionJun 27, 2025Deposition site: PDBJ / Processing site: PDBC
SupersessionAug 6, 2025ID: 6KFT
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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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
D: ASP-GLY-TYR-ILE-GLU-GLU-LEU-ILE-ARG-MET-PHE-GLY-LYS-LEU-SER-ILE-HIS-ASP-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,0509
Polymers160,3254
Non-polymers7255
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.920, 105.920, 303.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11C-1392-

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: 26496.279 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 (E. coli)
References: UniProt: P62826, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Protein Ran-specific GTPase-activating protein 1 / Chromosome stability protein 20 / Perinuclear array-localized protein / Ran-binding protein 1 / RANBP1


Mass: 16521.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08 / Production host: Escherichia coli (E. coli) / References: UniProt: P41920
#3: Protein Exportin-1 / Chromosome region maintenance protein 1 / Karyopherin-124


Mass: 115052.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: CRM1, KAP124, XPO1, YGR218W, G8514 / Production host: Escherichia coli (E. coli) / References: UniProt: P30822

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Protein/peptide , 1 types, 1 molecules D

#4: Protein/peptide ASP-GLY-TYR-ILE-GLU-GLU-LEU-ILE-ARG-MET-PHE-GLY-LYS-LEU-SER-ILE-HIS-ASP-ASP


Mass: 2254.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 289 molecules

#5: 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
#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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 300 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: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.45→86.85 Å / Num. obs: 64599 / % possible obs: 100 % / Redundancy: 25.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.153 / Net I/σ(I): 15.4
Reflection shellResolution: 2.45→2.51 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4681 / CC1/2: 0.634 / Rpim(I) all: 0.705

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→86.85 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 19.949 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.406 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23495 3209 5 %RANDOM
Rwork0.19779 ---
obs0.19962 61273 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.874 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å2-0 Å2-0 Å2
2--0.91 Å2-0 Å2
3----1.82 Å2
Refinement stepCycle: 1 / Resolution: 2.45→86.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10857 0 44 284 11185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01311122
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710464
X-RAY DIFFRACTIONr_angle_refined_deg1.2541.63815050
X-RAY DIFFRACTIONr_angle_other_deg1.1841.57524322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.00951340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47223.676574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.784152045
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2131551
X-RAY DIFFRACTIONr_chiral_restr0.0580.21472
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212191
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022238
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7225.3855372
X-RAY DIFFRACTIONr_mcbond_other1.7215.3845371
X-RAY DIFFRACTIONr_mcangle_it2.8328.0756705
X-RAY DIFFRACTIONr_mcangle_other2.8328.0766706
X-RAY DIFFRACTIONr_scbond_it2.0065.6435750
X-RAY DIFFRACTIONr_scbond_other2.0065.6415747
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4048.3528343
X-RAY DIFFRACTIONr_long_range_B_refined6.72646001
X-RAY DIFFRACTIONr_long_range_B_other6.7245902
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 234 -
Rwork0.372 4435 -
obs--99.74 %
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)
11.67380.8538-0.58812.8833-1.10343.5403-0.00730.14180.0041-0.0834-0.0709-0.2324-0.25980.31890.07830.0331-0.0191-0.01090.0688-0.02380.121757.206-4.83132.26
23.06661.8150.7835.37382.18176.2014-0.1068-0.09250.1543-0.0103-0.0279-0.0288-0.47370.28560.13470.2069-0.15460.00260.17360.05040.16360.10716.86317.363
30.3782-0.19090.06390.5329-0.04711.0724-0.00840.0569-0.05280.01980.0007-0.1021-0.0020.0290.00780.0086-0.0236-0.00190.08530.00180.159140.003-15.22230.79
46.19840.9109-1.75321.7147-0.34663.8010.204-0.2296-0.03450.1406-0.11650.2317-0.0611-0.0269-0.08750.28310.05510.0140.22680.01950.280214.57923.24429.383
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 216
2X-RAY DIFFRACTION1A301 - 302
3X-RAY DIFFRACTION2B80 - 200
4X-RAY DIFFRACTION3C0 - 1052
5X-RAY DIFFRACTION3C1101 - 1103
6X-RAY DIFFRACTION4D76 - 94

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