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- PDB-6xjt: Crystal Structure of KPT-8602 bound to CRM1 (537-DLTVK-541 to GLCEQ) -

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Basic information

Entry
Database: PDB / ID: 6xjt
TitleCrystal Structure of KPT-8602 bound to CRM1 (537-DLTVK-541 to GLCEQ)
Components
  • Exportin-1
  • GTP-binding nuclear protein Ran
  • Ran-specific GTPase-activating protein 1
KeywordsPROTEIN TRANSPORT / Nuclear export / CRM1 / XPO1 / Exportin-1
Function / homology
Function and homology information


positive regulation of mitotic centrosome separation / RNA nuclear export complex / pre-miRNA export from nucleus / nuclear export signal receptor activity / snRNA import into nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / cellular response to mineralocorticoid stimulus / Regulation of HSF1-mediated heat shock response / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) ...positive regulation of mitotic centrosome separation / RNA nuclear export complex / pre-miRNA export from nucleus / nuclear export signal receptor activity / snRNA import into nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / cellular response to mineralocorticoid stimulus / Regulation of HSF1-mediated heat shock response / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / SUMOylation of SUMOylation proteins / importin-alpha family protein binding / spindle pole body / protein localization to kinetochore / SUMOylation of RNA binding proteins / protein localization to nucleolus / U4 snRNA binding / Rev-mediated nuclear export of HIV RNA / nuclear export / Nuclear import of Rev protein / GTP metabolic process / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / RNA export from nucleus / SUMOylation of chromatin organization proteins / Postmitotic nuclear pore complex (NPC) reformation / 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 / ribosomal small subunit export from nucleus / U2 snRNA binding / U6 snRNA binding / mRNA export from nucleus / ribosomal subunit 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 / recycling endosome / kinetochore / small GTPase binding / positive regulation of protein import into nucleus / G1/S transition of mitotic cell cycle / 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 / cytoplasm / cytosol
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-6L8 / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 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: 2.406 Å
AuthorsBaumhardt, J.M. / Chook, Y.M.
Funding support2items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)
Welch Foundation
CitationJournal: J Hematol Oncol / Year: 2021
Title: Recurrent XPO1 mutations alter pathogenesis of chronic lymphocytic leukemia.
Authors: Walker, J.S. / Hing, Z.A. / Harrington, B. / Baumhardt, J. / Ozer, H.G. / Lehman, A. / Giacopelli, B. / Beaver, L. / Williams, K. / Skinner, J.N. / Cempre, C.B. / Sun, Q. / Shacham, S. / ...Authors: Walker, J.S. / Hing, Z.A. / Harrington, B. / Baumhardt, J. / Ozer, H.G. / Lehman, A. / Giacopelli, B. / Beaver, L. / Williams, K. / Skinner, J.N. / Cempre, C.B. / Sun, Q. / Shacham, S. / Stromberg, B.R. / Summers, M.K. / Abruzzo, L.V. / Rassenti, L. / Kipps, T.J. / Parikh, S. / Kay, N.E. / Rogers, K.A. / Woyach, J.A. / Coppola, V. / Chook, Y.M. / Oakes, C. / Byrd, J.C. / Lapalombella, R.
History
DepositionJun 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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)159,1966
Polymers158,2203
Non-polymers9773
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.675, 106.675, 306.070
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: 24456.105 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: 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, 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: 117442.812 Da / Num. of mol.: 1 / Mutation: 537-DLTVK-541 to GLCEQ
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CRM1, KAP124, XPO1, YGR218W, G8514 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30822

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Non-polymers , 3 types, 3 molecules

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


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
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
#6: Chemical ChemComp-6L8 / (2R)-3-{3-[3,5-bis(trifluoromethyl)phenyl]-1H-1,2,4-triazol-1-yl}-2-(pyrimidin-5-yl)propanamide


Mass: 430.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H12F6N6O / Feature type: SUBJECT OF INVESTIGATION

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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: 2.75 Å3/Da / Density % sol: 55.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 17% (weight/vol) PEG3350, 100 mM Bis-Tris (pH 6.4), 200 mM ammonium nitrate, and 10 mM Spermine HCl

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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: Jun 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 69620 / % possible obs: 100 % / Redundancy: 16.6 % / Biso Wilson estimate: 35.14 Å2 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.056 / Rrim(I) all: 0.14 / Χ2: 0.972 / Net I/σ(I): 5.4 / Num. measured all: 1152244
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.4-2.4416.433990.5760.9390.868100
2.44-2.4916.234260.6580.7710.868100
2.49-2.5316.134250.6790.6790.869100
2.53-2.5915.934390.7680.5750.889100
2.59-2.6414.434100.7790.4770.894100
2.64-2.715.834130.830.4110.948100
2.7-2.7717.334190.8980.3270.917100
2.77-2.8517.334370.9290.2580.929100
2.85-2.9317.234390.9540.2030.9551000.8210.847
2.93-3.0217.234780.9650.1610.9891000.6510.671
3.02-3.131734520.9770.1241.0521000.50.516
3.13-3.2616.934290.9850.0921.0611000.3690.381
3.26-3.4115.734800.9890.071.0971000.2720.281
3.41-3.5816.234810.9910.0541.1871000.2110.218
3.58-3.8117.934650.9940.041.2191000.1660.171
3.81-4.117.735210.9950.0321.2411000.1330.137
4.1-4.5217.334880.9960.0261.1361000.1040.107
4.52-5.1715.435750.9960.0220.9991000.0870.09
5.17-6.5117.635980.9980.0180.7531000.0740.077
6.51-5015.838460.9990.0120.53899.80.0470.049

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HB2

4hb2


Resolution: 2.406→45.545 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2461 2000 2.96 %
Rwork0.194 65652 -
obs0.1956 67652 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 181.04 Å2 / Biso mean: 49.3931 Å2 / Biso min: 9.79 Å2
Refinement stepCycle: final / Resolution: 2.406→45.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10818 0 87 0 10905
Biso mean--47.34 --
Num. residues----1341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01411350
X-RAY DIFFRACTIONf_angle_d1.21415406
X-RAY DIFFRACTIONf_chiral_restr0.0561753
X-RAY DIFFRACTIONf_plane_restr0.0081965
X-RAY DIFFRACTIONf_dihedral_angle_d16.9156889
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.406-2.46570.31361090.2421357976
2.4657-2.53240.33611320.2488433991
2.5324-2.60690.36241400.2415458697
2.6069-2.6910.29711400.2284458697
2.691-2.78720.27941450.2154768100
2.7872-2.89880.31681450.2174758100
2.8988-3.03070.26081460.23234792100
3.0307-3.19040.27411440.22654766100
3.1904-3.39020.2721460.21474782100
3.3902-3.65190.27211480.20384833100
3.6519-4.01920.23971470.17724841100
4.0192-4.60030.17681490.14754885100
4.6003-5.7940.19871500.16194946100
5.794-45.5450.20691590.17675191100
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)
10.0204-0.0232-0.01550.02680.01720.0110.00050.0345-0.0028-0.0044-0.014-0.0337-0.0015-0.0054-0.00660.1264-0.0489-0.00590.2021-0.11420.2461.25-8.285137.9705
20.03320.0117-0.02950.0092-0.00830.02480.00240.0628-0.0090.00020.0272-0.0375-0.02640.01390.00590.0889-0.09180.08610.274-0.14350.258262.8587-2.999731.7772
30.0122-0.00140.00370.00380.00240.0039-0.0169-0.01630.00680.0053-0.0122-0.0328-0.00860.0156-0.05040.0407-0.006-0.04280.2314-0.10830.340261.765-15.944737.0006
40.00050.0002-0.00050.0031-0.00010.00020.00740.0028-0.0271-0.0123-0.01-0.01540.0062-0.01490.00010.0368-0.0087-0.020.1914-0.09580.181751.901-18.749639.0633
50.02160.0103-0.00180.0039-0.00020-0.00550.0646-0.014-0.0119-0.0148-0.01820.0217-0.07310.00390.1016-0.0337-0.00990.3097-0.06610.183446.3404-9.990438.2955
60.03820.00370.01170.0047-0.00240.00750.05930.04160.03280.01690.0666-0.0073-0.0642-0.01920.01760.1728-0.08840.07030.2785-0.07020.182453.70963.736339.0244
70.00240.00010.0005-0.0001-00.0030.008-0.0047-0.00480.00450.0104-0.0105-0.0046-0.001-00.4611-0.05480.09840.5794-0.04340.47271.629521.625321.7575
80.00130.0009-0.00170-0.00030.0016-0.00860.0040.0037-0.0079-0.0109-0.00580.0035-0.012900.4541-0.06430.08450.5656-0.03560.39271.989510.21634.4769
90.0009-0.00020.00080.0015-0.00030.0006-0.01220.0092-0.00180.00810.00870.0028-0.00470.0034-00.3403-0.01380.08530.3712-0.08490.451151.32743.357912.3402
100.0611-0.02830.07190.0126-0.03290.08550.0094-0.0413-0.00650.042-0.0934-0.041-0.05380.0591-0.04170.3287-0.12040.17880.3749-0.05980.339560.338212.42719.9306
110.0013-0.00280.00410.0130.00990.0491-0.058-0.0006-0.033-0.0552-0.03580.0561-0.11360.0212-0.00630.4729-0.23650.11920.3755-0.09240.327860.355319.865924.7527
120.0109-0.00230.00630.02080.00980.00920.02980.0118-0.0134-0.08970.01050.0046-0.15640.15160.00070.5097-0.19650.15710.3961-0.07340.343260.557417.816812.5221
130.03430.05940.04240.19270.08940.06170.0194-0.0372-0.07770.2110.1526-0.47420.04320.32020.48740.06650.1725-0.25960.2932-0.10680.430563.9931-27.702253.0744
140.13280.04070.0260.18170.05270.22630.04970.0059-0.03350.09620.02610.0017-0.02360.01980.25530.095-0.01880.00280.1851-0.04180.07929.3519-1.880550.9027
150.07260.00950.02420.1510.02820.15010.04960.06510.0016-0.21720.0353-0.012-0.3209-0.10020.0180.29750.04580.02860.22720.02740.177826.27153.66097.5096
160.0767-0.03440.02860.058-0.05570.06970.07530.052-0.1699-0.11790.06160.046-0.03340.14590.01380.18220.0213-0.00690.1891-0.05050.225544.6313-35.51514.7592
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 22 )A9 - 22
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 66 )A23 - 66
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 91 )A67 - 91
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 111 )A92 - 111
5X-RAY DIFFRACTION5chain 'A' and (resid 112 through 148 )A112 - 148
6X-RAY DIFFRACTION6chain 'A' and (resid 149 through 179 )A149 - 179
7X-RAY DIFFRACTION7chain 'A' and (resid 180 through 189 )A180 - 189
8X-RAY DIFFRACTION8chain 'A' and (resid 190 through 206 )A190 - 206
9X-RAY DIFFRACTION9chain 'A' and (resid 207 through 216 )A207 - 216
10X-RAY DIFFRACTION10chain 'B' and (resid 78 through 106 )B78 - 106
11X-RAY DIFFRACTION11chain 'B' and (resid 107 through 139 )B107 - 139
12X-RAY DIFFRACTION12chain 'B' and (resid 140 through 200 )B140 - 200
13X-RAY DIFFRACTION13chain 'C' and (resid -1 through 245 )C-1 - 245
14X-RAY DIFFRACTION14chain 'C' and (resid 246 through 539 )C246 - 539
15X-RAY DIFFRACTION15chain 'C' and (resid 540 through 809 )C540 - 809
16X-RAY DIFFRACTION16chain 'C' and (resid 810 through 1052 )C810 - 1052

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