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- PDB-4wvf: Crystal structure of KPT276 in complex with CRM1-Ran-RanBP1 -

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Basic information

Entry
Database: PDB / ID: 4wvf
TitleCrystal structure of KPT276 in complex with CRM1-Ran-RanBP1
Components
  • Crm1p
  • GTP-binding nuclear protein Ran
  • Ran-specific GTPase-activating protein 1
KeywordsTRANSPORT PROTEIN/TRANSPORT PROTEIN INHIBITOR / CRM1 / inhibitor / SINE / KPT / TRANSPORT PROTEIN-TRANSPORT PROTEIN INHIBITOR complex
Function / homology
Function and homology information


RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / RNA export from nucleus / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA ...RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / RNA export from nucleus / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / GTP metabolic process / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / DNA metabolic process / NLS-bearing protein import into nucleus / dynein intermediate chain binding / ribosomal subunit export from nucleus / spermatid development / mitotic sister chromatid segregation / ribosomal small subunit export from nucleus / ribosomal large subunit export from nucleus / sperm flagellum / nuclear pore / protein export from nucleus / centriole / 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 / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / mitotic cell cycle / nuclear envelope / positive regulation of protein binding / midbody / ubiquitin-dependent protein catabolic process / actin cytoskeleton organization / cadherin binding / protein heterodimerization activity / cell division / protein domain specific binding / GTPase activity / chromatin binding / chromatin / GTP binding / nucleolus / 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 / 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like ...Ran-specific GTPase-activating protein 1, Ran-binding domain / 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 / 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 / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Chem-K76 / 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 / Resolution: 1.8 Å
AuthorsSun, Q. / Chook, Y.
CitationJournal: Nat.Neurosci. / Year: 2015
Title: Nuclear export inhibitors avert progression in preclinical models of inflammatory demyelination.
Authors: Haines, J.D. / Herbin, O. / de la Hera, B. / Vidaurre, O.G. / Moy, G.A. / Sun, Q. / Fung, H.Y. / Albrecht, S. / Alexandropoulos, K. / McCauley, D. / Chook, Y.M. / Kuhlmann, T. / Kidd, G.J. / ...Authors: Haines, J.D. / Herbin, O. / de la Hera, B. / Vidaurre, O.G. / Moy, G.A. / Sun, Q. / Fung, H.Y. / Albrecht, S. / Alexandropoulos, K. / McCauley, D. / Chook, Y.M. / Kuhlmann, T. / Kidd, G.J. / Shacham, S. / Casaccia, P.
History
DepositionNov 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id

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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: Crm1p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,82015
Polymers158,2493
Non-polymers1,57212
Water24,6631369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11450 Å2
ΔGint-62 kcal/mol
Surface area58060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.909, 105.909, 305.526
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Detailsbiological unit is the same as asym.

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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 (E. coli) / Strain (production host): BL21(DE3) / 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)
Strain: ATCC 204508 / S288c / Gene: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08 / Production host: Escherichia coli (E. coli) / References: UniProt: P41920
#3: Protein Crm1p


Mass: 117471.922 Da / Num. of mol.: 1 / Mutation: T539C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: R008 / Gene: Crm1, R008_G21866 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: W7PTE1

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Non-polymers , 7 types, 1381 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-K76 / (2E)-3-{3-[3,5-bis(trifluoromethyl)phenyl]-1H-1,2,4-triazol-1-yl}-1-(3,3-difluoroazetidin-1-yl)prop-2-en-1-one


Mass: 426.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H10F8N4O
#9: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1369 / Source method: isolated from a natural source / Formula: H2O

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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: 54.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 / Details: 0.1M Bis-Tris pH 6.6, 0.2M NH4NO3 and 18% PEG3350

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 159687 / % possible obs: 99.6 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.068 / Χ2: 1.362 / Net I/av σ(I): 33.892 / Net I/σ(I): 9.7 / Num. measured all: 1188877
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
1.8-1.833.575990.47596.3
1.83-1.863.977850.47798.6
1.86-1.94.578560.5199.60.939
1.9-1.945.379060.699.90.689
1.94-1.986.479090.58199.90.609
1.98-2.037.279380.611000.486
2.03-2.088.179290.6921000.396
2.08-2.138.479200.7441000.321
2.13-2.28.479730.7811000.266
2.2-2.278.579360.9811000.222
2.27-2.358.479521.0071000.177
2.35-2.448.579811.1071000.148
2.44-2.558.679491.2341000.123
2.55-2.698.680241.3781000.105
2.69-2.868.680441.561000.086
2.86-3.088.680181.8321000.072
3.08-3.398.681082.1999.90.061
3.39-3.888.481212.841000.057
3.88-4.88882373.15199.80.052
4.88-507.985022.15398.10.039

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
PDB_EXTRACT3.15data extraction
d*TREKdata scaling
MOLREPphasing
RefinementResolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.968 / SU B: 6.846 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1835 7989 5 %RANDOM
Rwork0.1365 151448 --
obs0.139 -99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 354.49 Å2 / Biso mean: 45.781 Å2 / Biso min: 22.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0 Å20 Å2
2---0.37 Å20 Å2
3---0.74 Å2
Refinement stepCycle: final / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10947 0 97 1369 12413
Biso mean--55.07 56.81 -
Num. residues----1356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01911500
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211145
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.96715617
X-RAY DIFFRACTIONr_angle_other_deg0.77325709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.02951419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94625.138545
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.899152123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5611552
X-RAY DIFFRACTIONr_chiral_restr0.0660.21781
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212900
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022600
X-RAY DIFFRACTIONr_mcbond_it4.0485511
X-RAY DIFFRACTIONr_mcbond_other4.0415510
X-RAY DIFFRACTIONr_mcangle_it4.7696907
X-RAY DIFFRACTIONr_rigid_bond_restr2.785311407
X-RAY DIFFRACTIONr_sphericity_free41.8465178
X-RAY DIFFRACTIONr_sphericity_bonded23.385511856
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 517 -
Rwork0.316 10056 -
all-10573 -
obs--90.19 %
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)
10.2632-0.0157-0.17220.7864-0.17011.02330.0440.09720.0249-0.00960.0436-0.1015-0.09090.0587-0.08760.0335-0.00940.00970.1479-0.01130.02564.012348.678832.2817
20.75590.1043-0.04811.72210.60861.4043-0.0181-0.1130.0292-0.0759-0.0053-0.0307-0.21280.19450.02340.1018-0.02670.03880.15410.02440.03665.960471.245120.1482
30.1183-0.04930.01020.29010.0630.40230.01580.008-0.00050.00620.014-0.0331-0.00670.0192-0.02980.0171-0.0145-0.00240.07210.00160.0056-12.926538.494830.9577
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 304
2X-RAY DIFFRACTION2B63 - 200
3X-RAY DIFFRACTION3C-1 - 1276

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