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- PDB-9ogo: Crystal Structure of KPT185 in complex with CRM1(EH mutant)-Ran-RanBP1 -

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Basic information

Entry
Database: PDB / ID: 9ogo
TitleCrystal Structure of KPT185 in complex with CRM1(EH mutant)-Ran-RanBP1
Components
  • Exportin-1
  • GTP-binding nuclear protein Ran
  • Ran-specific GTPase-activating protein 1
KeywordsTRANSPORT PROTEIN / Exportin / SINE / Export / XPO1
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 / Transcriptional and post-translational regulation of MITF-M expression and activity / manchette / nuclear export signal receptor activity / 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 / Transcriptional and post-translational regulation of MITF-M expression and activity / manchette / nuclear export signal receptor activity / 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 / tRNA processing in the nucleus / GTP metabolic process / 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 / U5 snRNA binding / spermatid development / viral process / ribosomal large subunit export from nucleus / 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 / 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 / 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 / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Chem-K85 / 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: 2.37 Å
AuthorsFung, H.Y.J. / Chook, Y.M.
Funding support United States, 7items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RP220582 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP180410 United States
Cancer Prevention and Research Institute of Texas (CPRIT)150053 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP170170 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM144137 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM131963 United States
Welch FoundationI-1532 United States
CitationJournal: To Be Published
Title: SINE compounds activate exportin-1 degradation via an allosteric mechanism
Authors: Wing, C.E. / Fung, H.Y.J. / Kwanten, B. / Cagatay, T. / Niesman, A.B. / Jacquelyn, M. / Gharghabi, M. / Permentier, B. / Shakya, B. / Ready, J.M. / Kashyap, T. / Shacham, S. / Landesman, Y. ...Authors: Wing, C.E. / Fung, H.Y.J. / Kwanten, B. / Cagatay, T. / Niesman, A.B. / Jacquelyn, M. / Gharghabi, M. / Permentier, B. / Shakya, B. / Ready, J.M. / Kashyap, T. / Shacham, S. / Landesman, Y. / Lapalombella, R. / Daelemans, D. / Chook, Y.M.
History
DepositionMay 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,8058
Polymers160,7733
Non-polymers1,0315
Water7,566420
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Purified complex
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9760 Å2
ΔGint-46 kcal/mol
Surface area57080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.077, 106.077, 303.933
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 26758.564 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: 16521.867 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: 117492.875 Da / Num. of mol.: 1 / Mutation: V529E, T539C, F572H, Y1022C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: CRM1, KAP124, XPO1, YGR218W, G8514 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30822

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Non-polymers , 6 types, 425 molecules

#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-K85 / propan-2-yl 3-{3-[3-methoxy-5-(trifluoromethyl)phenyl]-1H-1,2,4-triazol-1-yl}propanoate / KPT-185


Mass: 357.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18F3N3O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 53.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 17% PEG3350, 100 mM Bis-Tris (pH 6.6) and 200 mM ammonium nitrate

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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: Nov 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. obs: 71232 / % possible obs: 99.8 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.034 / Net I/av σ(I): 1.3 / Net I/σ(I): 19.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allΧ2% possible allRrim(I) all
2.37-2.418.1134850.5090.8210.4680.88599.3
2.41-2.458.3135030.5730.8540.3990.88599.7
2.45-2.58.30.97934850.6340.8810.3430.90799.9
2.5-2.558.30.85334940.6920.9050.2990.90299.90.907
2.55-2.618.20.73635050.7740.9340.2590.92999.90.783
2.61-2.678.20.63635080.8130.9470.2250.94199.90.678
2.67-2.748.20.5134900.8690.9640.180.93899.70.543
2.74-2.818.20.44235260.880.9670.1560.97199.80.471
2.81-2.898.20.36735200.9210.9790.130.97699.60.391
2.89-2.998.20.28435080.9570.9890.10.9899.90.302
2.99-3.098.30.22435320.9720.9930.0790.97899.60.238
3.09-3.228.20.17335400.9830.9960.0610.98999.70.185
3.22-3.368.30.12935210.9890.9970.0460.98399.70.137
3.36-3.548.30.09635820.9930.9980.0340.95999.80.102
3.54-3.768.40.07535640.9940.9990.0270.97199.90.08
3.76-4.058.70.06535890.9960.9990.0231.0661000.069
4.05-4.469.30.06236090.9950.9990.0211.3341000.066
4.46-5.110.40.05636320.9980.9990.0181.2571000.059
5.1-6.4311.20.04637010.99910.0140.8021000.048
6.43-50110.02239380.99910.0070.51499.90.023

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→40.24 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2000 3.01 %Random
Rwork0.193 ---
obs0.194 66474 93.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.37→40.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10780 0 65 420 11265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311076
X-RAY DIFFRACTIONf_angle_d0.46114985
X-RAY DIFFRACTIONf_dihedral_angle_d14.666712
X-RAY DIFFRACTIONf_chiral_restr0.0371707
X-RAY DIFFRACTIONf_plane_restr0.0031898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.371-2.43020.3004870.27812819X-RAY DIFFRACTION58
2.4302-2.49590.34661100.27013539X-RAY DIFFRACTION73
2.4959-2.56940.33371270.25724108X-RAY DIFFRACTION85
2.5694-2.65230.32671420.25154543X-RAY DIFFRACTION93
2.6523-2.74710.28891450.24524711X-RAY DIFFRACTION97
2.7471-2.8570.30821510.23724832X-RAY DIFFRACTION99
2.857-2.9870.26381500.21974849X-RAY DIFFRACTION100
2.987-3.14440.23281510.22024891X-RAY DIFFRACTION100
3.1444-3.34130.25821530.21464919X-RAY DIFFRACTION100
3.3413-3.59920.22051530.19154922X-RAY DIFFRACTION100
3.5992-3.96110.22211530.1664959X-RAY DIFFRACTION100
3.9611-4.53360.19661560.14875005X-RAY DIFFRACTION100
4.5336-5.70930.1771560.15445055X-RAY DIFFRACTION100
5.7093-40.240.21381660.17745322X-RAY DIFFRACTION100
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)
10.00840.0292-0.00180.0833-0.00670.005-0.00220.0207-0.0361-0.0410.0162-0.1442-0.04030.02140.00250.1355-0.11470.08010.3326-0.16170.41537.645447.583834.4361
20.012-0.01520.02380.0302-0.02840.04530.04650.137-0.1192-0.08050.0463-0.114-0.0132-0.0210.00330.3216-0.07750.20320.4424-0.19090.58417.474443.314622.9385
30.0247-0.0418-0.02030.1122-0.06040.2460.10770.0227-0.15410.1033-0.0133-0.1385-0.15830.19690.04670.2555-0.1020.04080.2974-0.15560.664311.606753.049938.6654
40.0349-0.0165-0.01820.0239-0.00750.02540.0571-0.0686-0.08290.04460.0438-0.21660.0099-0.00140.0683-0.05660.0907-0.18380.1882-0.11490.55818.287937.002338.0457
50.0149-0.0026-0.01240.0109-0.00440.0127-0.0239-0.0261-0.0135-0.09120.1555-0.15250.136-0.0122-00.222-0.0113-0.03910.2721-0.04310.4301-2.788834.359838.1893
60.05740.0334-0.08020.0502-0.02580.1131-0.00430.1297-0.084-0.00560.1213-0.20420.0492-0.15490.0690.1152-0.0294-0.07580.244-0.01040.3549-4.153242.148136.928
70.0417-0.02360.00220.02970.01990.01880.04270.03360.0646-0.02190.1192-0.0787-0.0258-0.0727-00.1714-0.0387-0.00190.2851-0.02430.2498-7.115946.677538.2068
80.1593-0.02770.11560.0221-0.04860.13740.194-0.10150.11060.05210.1215-0.0531-0.1183-0.0810.020.2786-0.03230.04370.2331-0.09370.28372.351758.440943.9778
90.0578-0.0780.00330.1068-0.00870.00620.0453-0.05260.0211-0.0293-0.0544-0.01250.04070.0227-0.0040.5221-0.37550.04790.8584-0.1070.527819.327870.490918.5185
100.0112-0.0140.00470.0128-0.00330.00660.05040.03150.006-0.02730.13880.0685-0.00960.0214-00.569-0.20040.1660.5788-0.18370.49846.020958.01278.5076
110.03120.02140.01440.01040.00520.0138-0.02220.0781-0.0592-0.00280.1363-0.0716-0.02670.015300.9172-0.1116-0.04790.9343-0.08760.72421.831182.643350.7715
120.0792-0.01620.13960.0105-0.03720.2481-0.0720.0091-0.10030.08950.036-0.0196-0.26350.1675-0.02730.4645-0.14070.18740.3572-0.09150.40997.130868.32721.9037
130.0414-0.0225-0.01570.18880.11690.0788-0.05470.2685-0.0635-0.2673-0.00070.1262-0.37220.2706-0.0010.6032-0.19140.08870.452-0.07440.36277.675570.427112.7691
140.19650.13750.10910.69410.09890.08490.1126-0.1987-0.28170.74230.1065-1.11010.19450.26490.69220.20060.1839-0.42620.3317-0.06990.90469.974224.837453.6493
150.5431-0.19630.23420.53630.33560.76180.12610.02510.05010.1197-0.0587-0.0459-0.0457-0.00350.44180.2032-0.0085-0.02190.2634-0.01560.1124-23.959652.121650.1848
160.16160.0748-0.06230.37970.03140.15010.1310.11160.1285-0.3050.0091-0.0747-0.6029-0.26290.24520.53930.11760.04580.41710.08420.2217-32.730563.443913.8079
170.4985-0.19950.16370.3803-0.21060.56430.02910.1193-0.2255-0.07420.10360.0789-0.01830.07290.37420.2301-0.01620.06210.2572-0.10510.2576-12.113427.90399.9703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 8 THROUGH 32 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 33 THROUGH 44 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 45 THROUGH 66 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 67 THROUGH 91 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 92 THROUGH 109 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 110 THROUGH 132 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 133 THROUGH 158 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 159 THROUGH 179 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 180 THROUGH 197 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 198 THROUGH 216 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 63 THROUGH 82 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 83 THROUGH 139 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 140 THROUGH 200 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 0 THROUGH 245 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 246 THROUGH 541 )
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 542 THROUGH 692 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 693 THROUGH 1053 )

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