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- PDB-6xjp: Crystal Structure of KPT-185 bound to CRM1 (537-DLTVK-541 to GLCEQ) -

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Basic information

Entry
Database: PDB / ID: 6xjp
TitleCrystal Structure of KPT-185 bound to CRM1 (537-DLTVK-541 to GLCEQ)
Components
  • Exportin-1Karyopherin
  • 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 / 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
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: 2.802 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)159,1236
Polymers158,2203
Non-polymers9043
Water0
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)105.947, 105.947, 305.497
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 / Karyopherin / 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 / 5'-Guanylyl imidodiphosphate


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-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

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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: 2.71 Å3/Da / Density % sol: 54.58 %
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, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 43873 / % possible obs: 100 % / Redundancy: 15.1 % / Biso Wilson estimate: 41.61 Å2 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.056 / Rrim(I) all: 0.185 / Χ2: 0.943 / Net I/σ(I): 5 / Num. measured all: 664242
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.8-2.8513.821430.6560.6080.8100
2.85-2.91321350.7290.5760.8100
2.9-2.9614.521550.7560.4680.79100
2.96-3.0215.621630.8150.3820.807100
3.02-3.0815.721360.8670.3110.828100
3.08-3.1515.621510.9240.2440.8591000.969
3.15-3.2315.521690.9220.2180.8721000.8660.895
3.23-3.3215.121600.9530.1660.9171000.6530.675
3.32-3.4214.921670.9650.1370.9611000.5350.553
3.42-3.5314.221710.970.1251.10199.90.4740.491
3.53-3.651421680.9690.1041.0811000.3910.406
3.65-3.815.821700.9820.0771.1331000.3090.318
3.8-3.9715.621690.9870.0651.2061000.2630.271
3.97-4.1815.521840.9860.0531.0931000.2160.222
4.18-4.4415.522130.990.0471.111000.1880.194
4.44-4.7914.321970.9870.0461.1151000.1730.179
4.79-5.2716.822360.9910.0380.9851000.1570.162
5.27-6.0316.722330.9930.0350.8481000.1450.15
6.03-7.5915.322980.9930.0330.7821000.1280.133
7.59-5015.224550.9870.030.77699.90.1150.12

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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: 2.802→46.995 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2604 1999 5.49 %
Rwork0.2146 34404 -
obs0.2172 36403 83.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 205.88 Å2 / Biso mean: 56.146 Å2 / Biso min: 0.29 Å2
Refinement stepCycle: final / Resolution: 2.802→46.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10791 0 70 0 10861
Biso mean--38.82 --
Num. residues----1338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311315
X-RAY DIFFRACTIONf_angle_d0.56915354
X-RAY DIFFRACTIONf_chiral_restr0.0391748
X-RAY DIFFRACTIONf_plane_restr0.0031958
X-RAY DIFFRACTIONf_dihedral_angle_d18.3556875
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.802-2.87180.3424470.28879828
2.8718-2.94940.3427610.2793106637
2.9494-3.03620.3336830.2824142149
3.0362-3.13410.37921070.2846182663
3.1341-3.24610.32241450.2677250486
3.2461-3.37610.30841660.2495287399
3.3761-3.52970.3181700.23282927100
3.5297-3.71570.26731690.21822907100
3.7157-3.94840.23941730.19762956100
3.9484-4.25310.23351710.17742953100
4.2531-4.68070.20341710.1612951100
4.6807-5.35720.22821750.17533000100
5.3572-6.74630.27221760.23623041100
6.7463-46.9950.23181850.2227318199
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)
10.02440.0108-0.01120.0047-0.0043-0.0006-0.04460.0703-0.0401-0.01070.0266-0.0396-0.02830.0217-0.0207-0.1243-0.10170.14580.2273-0.08070.052362.3938-4.00732.9871
20.0011-0.0010.00380.02990.0290.04120.038-0.0338-0.0368-0.0167-0.00190.00430.01240.0227-0.00190.1369-0.0244-0.06570.2722-0.02630.438664.7572-18.070936.8966
30.01510.00350.0070.0119-0.00080.01220.001-0.02720.00250.02680.0001-0.0420.03260.061-0.01060.09810.0287-0.05340.2271-0.0210.191452.1641-16.657838.2906
40.0212-0.01360.00120.0406-0.00220.0012-0.012-0.06670.05020.0226-0.0119-0.0466-0.0028-0.0042-0.08770.0043-0.0419-0.0930.1815-0.13060.087846.1543-10.651538.1339
50.03760.0008-0.02060.01790.02450.04390.05640.0232-0.01670.01240.00340.0015-0.04960.0245-0.0050.1917-0.0780.01950.2024-0.06750.205652.72612.681139.2291
60.0010.001-0.00320.00010.00050.0104-0.0013-0.01070.01130.0041-0.0002-0.01360.00460.000400.6138-0.12460.07650.6729-0.15830.597271.637421.551621.7414
70.00050.00140.000900.00110.0011-0.00460.0073-0.004-0.0116-0.0472-0.0105-0.0017-0.007300.5015-0.07510.01780.5126-0.04890.434671.685210.36974.5936
80.0015-0.0009-0.00050.0015-0.00040.0008-0.0018-0.0123-0.00130.0066-0.0142-0.00580.0043-0.01300.3874-0.06050.10470.4077-0.13610.508851.10863.670112.3792
90.0022-0.0028-0.0020.002-0.00490.0141-0.0112-0.0105-0.03220.024-0.025-0.0351-0.01440.0268-0.02360.3624-0.14210.1260.2035-0.04610.301158.737717.03522.2216
100.0022-0.00510.00190.0285-0.01390.01110.0373-0.0798-0.15940.01490.00280.0337-0.04530.06130.03130.4702-0.28670.19130.2267-0.06720.32161.090815.850922.5619
110.0062-0.00240.01240.0071-0.00760.0289-0.0016-0.00570.0256-0.02050.01940.0025-0.12630.11280.00370.5388-0.25220.19790.2536-0.01430.281560.454718.071612.6378
120.14230.094-0.01810.30310.11710.08030.0817-0.3569-0.13120.57160.0764-0.4360.09490.30120.62570.05020.1279-0.20370.33860.03010.39959.0687-24.869454.8712
130.19040.0081-0.14710.1340.05020.22170.3390.10370.1768-0.0488-0.0120.0516-0.3216-0.05551.329-0.08570.0555-0.14880.09750.0402-0.15824.54324.470141.1503
140.1446-0.0516-0.01660.1636-0.01220.1347-0.00510.1322-0.0191-0.22220.15760.0495-0.3674-0.2720.45590.35560.1398-0.03510.32840.1323-0.001928.24570.35830.6828
150.72080.04930.00290.35660.15960.3075-0.04210.1278-0.2709-0.16170.0909-0.02470.0010.1908-0.18780.1357-0.02420.01490.1746-0.06270.176844.2618-35.253514.5138
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 66 )A9 - 66
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 84 )A67 - 84
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 111 )A85 - 111
4X-RAY DIFFRACTION4chain 'A' and (resid 112 through 144 )A112 - 144
5X-RAY DIFFRACTION5chain 'A' and (resid 145 through 179 )A145 - 179
6X-RAY DIFFRACTION6chain 'A' and (resid 180 through 189 )A180 - 189
7X-RAY DIFFRACTION7chain 'A' and (resid 190 through 206 )A190 - 206
8X-RAY DIFFRACTION8chain 'A' and (resid 207 through 216 )A207 - 216
9X-RAY DIFFRACTION9chain 'B' and (resid 78 through 97 )B78 - 97
10X-RAY DIFFRACTION10chain 'B' and (resid 98 through 139 )B98 - 139
11X-RAY DIFFRACTION11chain 'B' and (resid 140 through 200 )B140 - 200
12X-RAY DIFFRACTION12chain 'C' and (resid -1 through 307 )C-1 - 307
13X-RAY DIFFRACTION13chain 'C' and (resid 308 through 611 )C308 - 611
14X-RAY DIFFRACTION14chain 'C' and (resid 612 through 808 )C612 - 808
15X-RAY DIFFRACTION15chain 'C' and (resid 809 through 1052 )C809 - 1052

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