- PDB-4gpt: Crystal structure of KPT251 in complex with CRM1-Ran-RanBP1 -
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Basic information
Entry
Database: PDB / ID: 4gpt
Title
Crystal structure of KPT251 in complex with CRM1-Ran-RanBP1
Components
Exportin-1
GTP-binding nuclear protein Ran
Ran-specific GTPase-activating protein 1
Keywords
PROTEIN TRANSPORT/INHIBITOR / HEAT repeat / protein nuclear export / KPT251 / nuclear / PROTEIN TRANSPORT-INHIBITOR complex
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 / 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 ...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 / 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 / tRNA export from nucleus / 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 / 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 / spindle pole body / 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 subunit export from nucleus / U2 snRNA binding / mRNA export from nucleus / U6 snRNA binding / nuclear pore / ribosomal small subunit export from nucleus / U1 snRNA binding / centriole / viral process / protein export from nucleus / 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 / 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / 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 nucleotide triphosphate hydrolases / Roll / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology
Chem-51K / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Exportin-1 / Ran-specific GTPase-activating protein 1 / GTP-binding nuclear protein Ran Similarity search - Component
Biological species
Homo sapiens (human) Saccharomyces cerevisiae (brewer's yeast)
Monochromator: Rosenbaum-Rock high-resolution double-crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 2.22→100.093 Å / Num. all: 86477 / Num. obs: 85858 / % possible obs: 99.3 %
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Processing
Software
Name
Version
Classification
HKL-3000
datacollection
CCP4
modelbuilding
REFMAC
5.6.0117
refinement
HKL-2000
datareduction
HKL-2000
datascaling
CCP4
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→50 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 10.506 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.20984
4323
5 %
RANDOM
Rwork
0.16471
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-
-
obs
0.16698
82020
99.34 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 57.385 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.01 Å2
0 Å2
0 Å2
2-
-
0.01 Å2
0 Å2
3-
-
-
-0.02 Å2
Refinement step
Cycle: LAST / Resolution: 2.22→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
10878
0
90
1287
12255
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.02
11485
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
7768
X-RAY DIFFRACTION
r_angle_refined_deg
1.18
1.966
15603
X-RAY DIFFRACTION
r_angle_other_deg
0.86
3
19090
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.183
5
1424
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.209
25.12
543
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.724
15
2120
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.062
15
52
X-RAY DIFFRACTION
r_chiral_restr
0.068
0.2
1776
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
12653
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
2270
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.22→2.278 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.385
287
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Rwork
0.364
5550
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obs
-
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99.59 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°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)
1
0.2589
0.3769
-0.3316
0.9294
-0.3231
1.2214
0.0424
0.0939
-0.0087
0.0307
0.1034
-0.0764
-0.0772
0.0582
-0.1458
0.0409
-0.0228
0.0074
0.2326
-0.047
0.0452
2.674
47.375
33.458
2
0.9184
0.546
-0.0604
2.6177
1.4283
3.1163
-0.0356
-0.0429
-0.0561
-0.356
0.0318
0.0207
-0.586
0.3112
0.0038
0.2594
-0.146
0.0628
0.1764
-0.0101
0.0438
6.467
70.025
17.059
3
0.204
-0.1424
-0.0262
0.3951
0.1027
0.559
0.0328
0.0037
0.0056
0.0013
0.0205
-0.0511
-0.0289
0.0294
-0.0533
0.0278
-0.0205
-0.0009
0.1245
-0.0068
0.0106
-12.874
38.285
31.29
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
9 - 216
2
X-RAY DIFFRACTION
1
A
301 - 302
3
X-RAY DIFFRACTION
2
B
78 - 200
4
X-RAY DIFFRACTION
3
C
-1 - 1052
5
X-RAY DIFFRACTION
3
C
1101
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