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- PDB-6xjr: Crystal Structure of KPT-185 bound to CRM1 (E582K, 537-DLTVK-541 ... -

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Basic information

Entry
Database: PDB / ID: 6xjr
TitleCrystal Structure of KPT-185 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 / Regulation of cholesterol biosynthesis by SREBP (SREBF) / tRNA export from nucleus / 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 / 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 / SUMOylation of chromatin organization proteins / 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 / nuclear pore / ribosomal subunit export from nucleus / 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 / 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, 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 / 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: 1.941 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
Revision 1.2Nov 6, 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)159,1236
Polymers158,2203
Non-polymers9043
Water20,6631147
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)105.992, 105.992, 306.033
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 , 4 types, 1150 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-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1147 / 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: 2.72 Å3/Da / Density % sol: 54.7 %
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: 123500 / % possible obs: 95.5 % / Redundancy: 17.6 % / Biso Wilson estimate: 18.77 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.021 / Rrim(I) all: 0.092 / Χ2: 0.993 / Net I/σ(I): 8.8 / Num. measured all: 2178775
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.94-1.9717.92.92358210.4860.6630.87691.1
1.97-2.0117.82.41157560.640.5472.4750.87690.9
2.01-2.0517.61.92557740.7180.4411.9770.88290.6
2.05-2.0917.21.49757800.8070.3471.5390.96190.3
2.09-2.1416.81.18457350.8520.2791.2180.91390.2
2.14-2.1815.40.96957770.8730.240.9990.92490.5
2.18-2.2417.20.78558160.9360.1810.8070.94291
2.24-2.317.10.58559280.9580.1340.61.03492.1
2.3-2.3716.80.45959460.9750.1060.4710.99293.5
2.37-2.4416.20.3661170.9840.0840.371.0195.6
2.44-2.5315.60.27462250.9880.0650.2821.04396.8
2.53-2.6314.70.21563100.9910.0530.2221.05998
2.63-2.7515.80.16463380.9940.0390.1691.07998.7
2.75-2.916.90.12464610.9960.0290.1271.06599.9
2.9-3.0817.80.09564770.9970.0220.0981.081100
3.08-3.3218.50.07565070.9980.0170.0771.124100
3.32-3.6519.10.06265180.9990.0140.0641.20599.7
3.65-4.18220.05465490.9990.0120.0551.212100
4.18-5.2620.60.04566530.9990.010.0461.01599.8
5.26-4020.80.02870120.9990.0060.0280.56799.9

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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: 1.941→38.254 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2263 2000 1.72 %
Rwork0.1935 114267 -
obs0.1941 116267 89.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 170.82 Å2 / Biso mean: 36.3419 Å2 / Biso min: 1.59 Å2
Refinement stepCycle: final / Resolution: 1.941→38.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10794 0 70 1147 12011
Biso mean--28.68 36.95 -
Num. residues----1339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311336
X-RAY DIFFRACTIONf_angle_d0.5515390
X-RAY DIFFRACTIONf_chiral_restr0.0391752
X-RAY DIFFRACTIONf_plane_restr0.0031963
X-RAY DIFFRACTIONf_dihedral_angle_d16.336888
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9413-1.98990.2601630.2664361040
1.9899-2.04360.34091180.2454669174
2.0436-2.10380.28381280.2359734882
2.1038-2.17170.25421380.2218785787
2.1717-2.24930.25811400.2131805990
2.2493-2.33930.24631450.1998828892
2.3393-2.44580.24891500.1985853895
2.4458-2.57470.24261540.1943877697
2.5747-2.7360.23771550.1956888398
2.736-2.94720.22531590.19759072100
2.9472-3.24360.22551590.1999085100
3.2436-3.71260.23161600.17889132100
3.7126-4.67620.16681620.15599278100
4.6762-38.2540.20681690.19369650100
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)
10.02590.0011-0.00690.0065-0.00320.00640.00210.0003-0.00460.0035-0.0034-0.0033-0.00580.0024-0.00460.0219-0.0339-0.00030.1514-0.07420.12261.23-8.19137.872
20.00690.0045-0.00330.0019-0.00110.0020.01330.0057-0.00080.00130.0108-0.0147-0.02290.02710.02060.0175-0.13380.04680.186-0.10830.134662.745-2.87231.696
30.00070.00040.00060.00450.00230.00190.0019-0.0058-0.0053-0.0043-0.0031-0.00870.00420.0086-0.00390.03220.0085-0.0280.1805-0.10540.191964.206-20.08634.352
40.00830.00160.00530.00680.00530.0068-0.0021-0.00840.00220.01220.0013-0.0165-0.00080.01-0.00270.0137-0.0353-0.03460.1135-0.06690.11758.404-10.04540.334
50.0202-0.00630.0010.0133-0.00770.0084-0.00640.0106-0.0099-0.00580.0011-0.00220.0065-0.0025-0.0082-0.004-0.0032-0.05180.1132-0.05830.117351.982-18.67538.793
60.00540.0023-0.00260.0007-0.00130.0050.0013-0.0015-0.0007-0.00880.00410.02240.0052-0.00880.0056-0.0696-0.0488-0.03360.1254-0.06750.068646.33-9.88838.287
70.0035-0.00010.00280.0001-0.00180.00330.01060.00440.01760.00570.01080.0069-0.0070.00070.01760.0164-0.08360.05220.0981-0.03810.07252.670.85537.33
80.0005-0.0001-0.00030.00060.00010.00060.0002-0.00170.00170.00360.00040.00290.0001-0.0017-00.3103-0.0340.07490.2928-0.02780.2956.19210.71643.222
90.00110.0007-0.00150.000400.00610.0025-0.0050.00230.0008-0.002-0.00050.0014-0.001900.3362-0.0590.0290.3624-0.00610.333971.54421.50321.743
100.00010.0001-0.00030.00020.00060.0009-0.00610.0030.00210.0021-0.0109-0.00520.0051-0.007100.3374-0.04090.03850.3414-0.02640.311872.38910.8464.56
110.00270.0004-0.00140.00070.00070.0015-0.004-0.00310-0.00140.00130.0012-0.0032-0.0029-00.2275-0.07030.01680.2189-0.04720.256352.0143.74311.515
120.00010.00030.00030.0045-0.00070.00180-00.000500.0002-0.0006-0.0009-0.000400.7106-0.00830.00190.7052-0.00230.712862.28225.53433.272
130.0030.0022-0.00140.0016-0.00150.0025-0.0107-0.0027-0.00340.0069-0.00810.0016-0.02450.012400.2452-0.11240.08860.2069-0.04320.22259.8610.16917.506
140.0031-0.001-0.0040.0009-0.00040.0126-0.0094-0.0051-0.0054-0.0039-0.00540.0099-0.02550.0079-0.00870.2758-0.20210.10250.2133-0.07620.246360.28519.95624.918
150.0010.00230.00040.00830.00070.0078-0.0015-0.0010.0068-0.0270.00120.0018-0.04830.0399-0.0040.3364-0.18810.12080.2007-0.05460.223360.45218.00312.678
160.01960.01940.03160.05420.04120.02380.04320.0169-0.0590.22480.1312-0.32620.06110.25090.3002-0.16550.2081-0.26530.2097-0.07350.179362.086-27.06453.519
170.154-0.032-0.10790.15490.0290.11240.1860.0430.2023-0.0971-0.02490.0823-0.1456-0.08520.3386-0.15480.0502-0.07270.07540.0179-0.073225.1014.00435.852
180.3337-0.04280.00810.16610.05790.21970.04930.1133-0.1501-0.18940.0763-0.0195-0.07790.05820.43340.00160.00280.01590.1189-0.04350.064941.166-25.3869.231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 9:22 )A9 - 22
2X-RAY DIFFRACTION2( CHAIN A AND RESID 23:66 )A23 - 66
3X-RAY DIFFRACTION3( CHAIN A AND RESID 67:80 )A67 - 80
4X-RAY DIFFRACTION4( CHAIN A AND RESID 81:91 )A81 - 91
5X-RAY DIFFRACTION5( CHAIN A AND RESID 92:111 )A92 - 111
6X-RAY DIFFRACTION6( CHAIN A AND RESID 112:148 )A112 - 148
7X-RAY DIFFRACTION7( CHAIN A AND RESID 149:169 )A149 - 169
8X-RAY DIFFRACTION8( CHAIN A AND RESID 170:179 )A170 - 179
9X-RAY DIFFRACTION9( CHAIN A AND RESID 180:187 )A180 - 187
10X-RAY DIFFRACTION10( CHAIN A AND RESID 190:205 )A190 - 205
11X-RAY DIFFRACTION11( CHAIN A AND RESID 206:216 )A206 - 216
12X-RAY DIFFRACTION12( CHAIN B AND RESID 78:82 )B78 - 82
13X-RAY DIFFRACTION13( CHAIN B AND RESID 83:106 )B83 - 106
14X-RAY DIFFRACTION14( CHAIN B AND RESID 107:139 )B107 - 139
15X-RAY DIFFRACTION15( CHAIN B AND RESID 140:200 )B140 - 200
16X-RAY DIFFRACTION16( CHAIN C AND RESID -1:268 )C-1 - 268
17X-RAY DIFFRACTION17( CHAIN C AND RESID 269:692 )C269 - 692
18X-RAY DIFFRACTION18( CHAIN C AND RESID 693:1052 )C693 - 1052

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