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- PDB-6xjs: Crystal Structure of KPT-330 bound to CRM1 (E582K, 537-DLTVK-541 ... -

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Basic information

Entry
Database: PDB / ID: 6xjs
TitleCrystal Structure of KPT-330 bound to CRM1 (E582K, 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


Transcriptional and post-translational regulation of MITF-M expression and activity / tRNA re-export from nucleus / RNA nuclear export complex / pre-miRNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear export signal receptor activity / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response / manchette / cellular response to mineralocorticoid stimulus ...Transcriptional and post-translational regulation of MITF-M expression and activity / tRNA re-export from nucleus / RNA nuclear export complex / pre-miRNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear export signal receptor activity / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response / manchette / cellular response to mineralocorticoid stimulus / tRNA export from nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / SUMOylation of SUMOylation proteins / importin-alpha family protein binding / protein localization to kinetochore / SUMOylation of RNA binding proteins / protein localization to nucleolus / U4 snRNA binding / SUMOylation of chromatin organization proteins / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / nuclear export / RNA export from nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / GTP metabolic process / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / spindle pole body / 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 / viral process / mRNA export from nucleus / U2 snRNA binding / U6 snRNA binding / ribosomal subunit export from nucleus / nuclear pore / ribosomal small subunit export from nucleus / U1 snRNA binding / protein export from nucleus / centriole / GTPase activator activity / mitotic spindle organization / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / recycling endosome / G protein activity / kinetochore / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / G1/S transition of mitotic cell cycle / GDP binding / melanosome / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / midbody / actin cytoskeleton organization / 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 / nucleolus / 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, 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 domain / Ran binding protein RanBP1-like / 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 / selinexor, bound form / 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: 1.942 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)159,3968
Polymers158,2203
Non-polymers1,1765
Water9,152508
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)106.044, 106.044, 305.622
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: 117442.875 Da / Num. of mol.: 1 / Mutation: E582K, 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 , 5 types, 513 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-V6A / selinexor, bound form / 3-{3-[3,5-bis(trifluoromethyl)phenyl]-1H-1,2,4-triazol-1-yl}-N'-(pyrazin-2-yl)propanehydrazide


Mass: 445.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H13F6N7O / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 2.71 Å3/Da / Density % sol: 54.68 %
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: 1.94→40 Å / Num. obs: 166432 / % possible obs: 100 % / Redundancy: 17.2 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.025 / Rrim(I) all: 0.106 / Χ2: 0.99 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.94-1.9716.33.27364180.4770.8093.3750.956100
1.97-2.01172.55463500.5640.6192.6310.95100
2.01-2.0516.91.95763560.6630.4752.0160.953100
2.05-2.0916.61.57663810.7690.3851.6240.967100
2.09-2.1416.51.24363790.8440.3061.2820.971100
2.14-2.1816.11.00163700.8790.2491.0330.953100
2.18-2.2415.80.79963840.9220.2010.8250.97399.9
2.24-2.315.20.61264210.9460.1570.6330.973100
2.3-2.3714.30.48263700.9650.1280.50.954100
2.37-2.4416.50.39164170.9810.0960.4030.96100
2.44-2.5316.40.30564160.9860.0750.3140.96100
2.53-2.6316.40.23964280.9890.0590.2460.961100
2.63-2.7516.40.18464210.9930.0450.1890.952100
2.75-2.916.40.13364630.9960.0330.1370.94100
2.9-3.0815.60.09864720.9970.0250.1020.972100
3.08-3.3219.10.07265170.9980.0170.0741.029100
3.32-3.6520.10.05365310.9990.0120.0551.104100
3.65-4.1820.70.04165570.9990.0090.0421.134100
4.18-5.2620.80.03466610.9990.0080.0351.092100
5.26-4020.50.028701610.0060.0290.94399.9

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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: 1.942→38.203 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2402 2806 1.69 %
Rwork0.2015 163626 -
obs0.2021 166432 67.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 193.31 Å2 / Biso mean: 52.7648 Å2 / Biso min: 1.21 Å2
Refinement stepCycle: final / Resolution: 1.942→38.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10818 0 90 508 11416
Biso mean--36.39 46.32 -
Num. residues----1342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311352
X-RAY DIFFRACTIONf_angle_d0.55815410
X-RAY DIFFRACTIONf_chiral_restr0.0391752
X-RAY DIFFRACTIONf_plane_restr0.0031964
X-RAY DIFFRACTIONf_dihedral_angle_d16.6166896
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.942-1.97510.3906460.302270422
1.9751-2.01110.3086580.2895341328
2.0111-2.04970.3071760.2785447637
2.0497-2.09160.2928940.2699548945
2.0916-2.13710.27991020.2664601050
2.1371-2.18680.30841040.2575613251
2.1868-2.24140.29661060.2522623852
2.2414-2.3020.27911070.2487628852
2.302-2.36980.22051060.2386625152
2.3698-2.44620.2911070.2296640053
2.4462-2.53370.24251200.2178679856
2.5337-2.63510.25691430.2155876972
2.6351-2.7550.24691810.22191040886
2.755-2.90020.24532050.22191176497
2.9002-3.08180.24122140.219512059100
3.0818-3.31960.28852100.209312100100
3.3196-3.65350.26122090.1912101100
3.6535-4.18160.20012070.164412042100
4.1816-5.26610.18572050.148812101100
5.2661-38.2030.20892060.185612083100
Refinement TLS params.Method: refined / Origin x: 44.7666 Å / Origin y: -9.9666 Å / Origin z: 30.2435 Å
111213212223313233
T-0.1023 Å2-0.0187 Å2-0.0016 Å2-0.0216 Å2-0.0303 Å2---0.0593 Å2
L0.0628 °20.0044 °2-0.0013 °2-0.0468 °20.0698 °2--0.1693 °2
S0.142 Å °0.0048 Å °-0.0231 Å °-0.0188 Å °0.0765 Å °-0.1095 Å °-0.0986 Å °0.0379 Å °0.2908 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA9 - 302
2X-RAY DIFFRACTION1allB78 - 200
3X-RAY DIFFRACTION1allC-1 - 1052
4X-RAY DIFFRACTION1allD1
5X-RAY DIFFRACTION1allD3
6X-RAY DIFFRACTION1allE1
7X-RAY DIFFRACTION1allS1 - 508

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