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- PDB-4ol0: Crystal structure of transportin-SR2, a karyopherin involved in h... -

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Basic information

Entry
Database: PDB / ID: 4ol0
TitleCrystal structure of transportin-SR2, a karyopherin involved in human disease, in complex with Ran
Components
  • GTP-binding nuclear protein Ran
  • Transportin-3
KeywordsPROTEIN TRANSPORT / Human Karyopherins / Active Transport / Nucleus / ran GTP-Binding Protein
Function / homology
Function and homology information


annulate lamellae / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / GTP metabolic process ...annulate lamellae / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / GTP metabolic process / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / MicroRNA (miRNA) biogenesis / DNA metabolic process / mitotic sister chromatid segregation / ribosomal large subunit export from nucleus / viral process / nuclear pore / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / centriole / protein export from nucleus / mitotic spindle organization / Transcriptional regulation by small RNAs / recycling endosome / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / positive regulation of protein binding / nuclear envelope / melanosome / mitotic cell cycle / G protein activity / midbody / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cadherin binding / protein heterodimerization activity / cell division / GTPase activity / chromatin binding / GTP binding / chromatin / nucleolus / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Transportin-3/Importin-13 second TPR domain / Transportin-3/Importin-13 third TPR domain / Transportin-3/Importin-13 fourth TPR domain / : / Exportin-1/Importin-beta-like / Exportin 1-like protein / small GTPase Ran family profile. / Ran GTPase / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases ...Transportin-3/Importin-13 second TPR domain / Transportin-3/Importin-13 third TPR domain / Transportin-3/Importin-13 fourth TPR domain / : / Exportin-1/Importin-beta-like / Exportin 1-like protein / small GTPase Ran family profile. / Ran GTPase / 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 / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / GTP-binding nuclear protein Ran / Transportin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTsirkone, V.G. / Strelkov, S.V.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Structure of transportin SR2, a karyopherin involved in human disease, in complex with Ran.
Authors: Tsirkone, V.G. / Beutels, K.G. / Demeulemeester, J. / Debyser, Z. / Christ, F. / Strelkov, S.V.
History
DepositionJan 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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: Transportin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,0564
Polymers128,5092
Non-polymers5472
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-11 kcal/mol
Surface area46090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.202, 109.970, 148.462
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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 / Plasmid: pETSUK / Production host: Escherichia coli (E. coli) / References: UniProt: P62826
#2: Protein Transportin-3 / Importin-12 / Imp12 / Transportin-SR / TRN-SR


Mass: 104052.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNPO3, IPO12 / Plasmid: pETSUK / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5L0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 100mM MES, 4.8% MPD, 15.2% PEG6000, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→44.18 Å / Num. obs: 27515 / % possible obs: 99.3 %
Reflection shellHighest resolution: 2.9 Å

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→44.184 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 28.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2757 1381 5.02 %
Rwork0.2218 --
obs0.2244 27515 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→44.184 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8559 0 33 33 8625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038768
X-RAY DIFFRACTIONf_angle_d0.78611902
X-RAY DIFFRACTIONf_dihedral_angle_d14.9093241
X-RAY DIFFRACTIONf_chiral_restr0.0291377
X-RAY DIFFRACTIONf_plane_restr0.0031512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.00370.34041420.30132559X-RAY DIFFRACTION100
3.0037-3.12390.36161370.292597X-RAY DIFFRACTION100
3.1239-3.26610.32781300.27532589X-RAY DIFFRACTION100
3.2661-3.43820.31591470.26412578X-RAY DIFFRACTION100
3.4382-3.65350.30771330.23792593X-RAY DIFFRACTION100
3.6535-3.93540.29721290.22142627X-RAY DIFFRACTION100
3.9354-4.33120.29161410.19782590X-RAY DIFFRACTION100
4.3312-4.95720.23021370.1842640X-RAY DIFFRACTION100
4.9572-6.24270.24511430.2332639X-RAY DIFFRACTION99
6.2427-44.1890.231420.1892722X-RAY DIFFRACTION98

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