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- PDB-8hq6: KL2 in complex with CRM1-Ran-RanBP1 -

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Basic information

Entry
Database: PDB / ID: 8hq6
TitleKL2 in complex with CRM1-Ran-RanBP1
Components
  • CRM1 isoform 1
  • GTP-binding nuclear protein Ran
  • YRB1 isoform 1
KeywordsTRANSPORT PROTEIN / nuclear export inhibitor
Function / homology
Function and homology information


positive regulation of mitotic centrosome separation / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / import into nucleus / nuclear export signal receptor activity / Regulation of cholesterol biosynthesis by SREBP (SREBF) / NLS-bearing protein import into nucleus / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA ...positive regulation of mitotic centrosome separation / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / import into nucleus / nuclear export signal receptor activity / Regulation of cholesterol biosynthesis by SREBP (SREBF) / NLS-bearing protein import into nucleus / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / GTP metabolic process / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / DNA metabolic process / mitotic sister chromatid segregation / ribosomal large subunit export from nucleus / viral process / nuclear pore / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / centriole / GTPase activator activity / protein export from nucleus / mitotic spindle organization / Transcriptional regulation by small RNAs / recycling endosome / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / positive regulation of protein binding / melanosome / nuclear envelope / mitotic cell cycle / G protein activity / midbody / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cadherin binding / protein heterodimerization activity / cell division / GTPase activity / chromatin binding / GTP binding / chromatin / nucleolus / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / nucleus / membrane / 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 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 / 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
GLUTAMIC ACID / GUANOSINE-5'-TRIPHOSPHATE / Chem-MFF / NITRATE ION / YRB1 isoform 1 / CRM1 isoform 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: 2.03 Å
AuthorsSun, Q. / Jian, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2023
Title: Discovery of Aminoratjadone Derivatives as Potent Noncovalent CRM1 Inhibitors.
Authors: Jian, L. / Zscherp, R. / Beutling, U. / Shen, X. / Xu, S. / Zhang, X. / Bronstrup, M. / Klahn, P. / Sun, Q.
History
DepositionDec 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2023Provider: 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: YRB1 isoform 1
C: CRM1 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,85532
Polymers155,9443
Non-polymers2,91129
Water12,412689
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14390 Å2
ΔGint-41 kcal/mol
Surface area55700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.752, 104.752, 302.806
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-1222-

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: 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 YRB1 isoform 1


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, GI526_G0000915 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5PZB5
#3: Protein CRM1 isoform 1 / HLJ1_G0022020.mRNA.1.CDS.1 / Y55_G0022260.mRNA.1.CDS.1


Mass: 115224.461 Da / Num. of mol.: 1
Mutation: S27E , Q49E, A51V, del377-413, del441-461, D537G, T539C, V540E, K541Q, S553R, Q561E, A741T, Y1022C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CRM1, GI526_G0002640, PACBIOSEQ_LOCUS2878, PACBIOSEQ_LOCUS3002
Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5PZI8

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Non-polymers , 9 types, 718 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 62.005 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: NO3
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: 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
#8: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#10: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#11: Chemical ChemComp-MFF / methyl (3~{S},5~{R},6~{E},8~{Z},10~{R},12~{E},14~{E},16~{S})-3,16-bis(azanyl)-8,10,12-trimethyl-16-[(2~{S},4~{R},5~{S},6~{S})-5-methyl-4-oxidanyl-6-[(~{E})-prop-1-enyl]oxan-2-yl]-5-oxidanyl-hexadeca-6,8,12,14-tetraenoate


Mass: 504.702 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H48N2O5 / Feature type: SUBJECT OF INVESTIGATION
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 689 / 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: 2.66 Å3/Da / Density % sol: 53.82 %
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: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.03→104.72 Å / Num. obs: 109668 / % possible obs: 100 % / Redundancy: 23.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.02 / Rrim(I) all: 0.1 / Χ2: 0.8 / Net I/σ(I): 14.4 / Num. measured all: 2544794
Reflection shellResolution: 2.03→2.08 Å / % possible obs: 100 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.944 / Num. measured all: 96031 / Num. unique obs: 7943 / CC1/2: 0.842 / Rpim(I) all: 0.275 / Rrim(I) all: 0.986 / Χ2: 0.62 / Net I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
REFMAC5refinement
Aimlessdata scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→99.19 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 8.833 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22414 5496 5 %RANDOM
Rwork0.19102 ---
obs0.1927 103907 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.985 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å2-0 Å2-0 Å2
2--1.03 Å2-0 Å2
3----2.07 Å2
Refinement stepCycle: 1 / Resolution: 2.03→99.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10759 0 182 689 11630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01311178
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710534
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.64715103
X-RAY DIFFRACTIONr_angle_other_deg1.3811.5824474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48251336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16323.644568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.772152039
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0321551
X-RAY DIFFRACTIONr_chiral_restr0.0780.21473
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212207
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022239
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_it1.6733.1285350
X-RAY DIFFRACTIONr_mcbond_other1.6733.1285351
X-RAY DIFFRACTIONr_mcangle_it2.5724.6816682
X-RAY DIFFRACTIONr_mcangle_other2.5724.6826683
X-RAY DIFFRACTIONr_scbond_it2.3323.4985828
X-RAY DIFFRACTIONr_scbond_other2.3323.4995829
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7325.1048422
X-RAY DIFFRACTIONr_long_range_B_refined7.18460.16448894
X-RAY DIFFRACTIONr_long_range_B_other7.13659.86848506
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.03→2.083 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 423 -
Rwork0.26 7478 -
obs--99.47 %
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)
12.08990.55980.61481.60510.82683.26190.0806-0.08180.09550.1041-0.0414-0.0987-0.29170.2776-0.03920.0549-0.0420.00970.03930.00510.0744-4.80356.438-32.142
20.2003-0.30210.68391.0044-1.38575.73220.05660.0646-0.0538-0.0664-0.05890.0363-0.07270.64130.00230.1548-0.1695-0.03420.2865-0.00820.274817.24459.471-19.152
30.4352-0.2248-0.02750.3496-0.07250.9036-0.00240.0210.04420.0486-0.01620.0293-0.09130.00230.01850.0613-0.0222-0.01010.0131-0.0060.1158-14.81639.508-30.682
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 216
2X-RAY DIFFRACTION2B65 - 201
3X-RAY DIFFRACTION3C0 - 1052

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