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- PDB-3ibv: Karyopherin cytosolic state -

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Basic information

Entry
Database: PDB / ID: 3ibv
TitleKaryopherin cytosolic state
ComponentsExportin-T
KeywordsRNA BINDING PROTEIN / karyopherin / exportin / HEAT repeat / Cytoplasm / Nucleus / RNA-binding / Transport / tRNA processing / tRNA-binding
Function / homology
Function and homology information


tRNA re-export from nucleus / nuclear export signal receptor activity / tRNA export from nucleus / tRNA processing / nuclear pore / small GTPase binding / nuclear matrix / nuclear envelope / tRNA binding / GTP binding ...tRNA re-export from nucleus / nuclear export signal receptor activity / tRNA export from nucleus / tRNA processing / nuclear pore / small GTPase binding / nuclear matrix / nuclear envelope / tRNA binding / GTP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Exportin-T / Exportin-T, C-terminal domain / Exportin-T / Exportin-1/Importin-beta-like / Exportin 1-like protein / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.1 Å
AuthorsCook, A.G. / Fukuhara, N. / Jinek, M. / Conti, E.
CitationJournal: Nature / Year: 2009
Title: Structures of the tRNA export factor in the nuclear and cytosolic states
Authors: Cook, A.G. / Fukuhara, N. / Jinek, M. / Conti, E.
History
DepositionJul 17, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Exportin-T
B: Exportin-T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,8706
Polymers220,7102
Non-polymers1604
Water00
1
A: Exportin-T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,4353
Polymers110,3551
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exportin-T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,4353
Polymers110,3551
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.900, 130.100, 173.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Exportin-T / tRNA exportin / Exportin(tRNA) / Karyopherin-beta


Mass: 110354.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: los1, SPBP8B7.09c / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O94258
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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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: 3.07 Å3/Da / Density % sol: 59.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM MES, pH6.5, 30% PEG400, 160mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA10.96
SYNCHROTRONSLS X10SA21.037
SYNCHROTRONSLS X10SA31.006
SYNCHROTRONSLS X10SA40.978
Detector
TypeIDDetectorDate
PSI PILATUS 6M1PIXELApr 24, 2008
MARMOSAIC 225 mm CCD2CCDMay 19, 2007
MARMOSAIC 225 mm CCD3CCDMay 19, 2007
MARMOSAIC 225 mm CCD4CCDOct 31, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
3SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
4SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.961
21.0371
31.0061
40.9781
ReflectionResolution: 3.1→49.9 Å / Num. obs: 48907 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 87.232 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 17.22
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
3.1-3.20.752.319853410792.4
3.2-3.40.665462800685391.5
3.4-3.80.4377.91369641051599
3.8-40.22213.450348385499.9
4-4.30.14918.159749451299.9
4.3-4.50.10823.633106239199.9
4.5-50.09326.2601894445100
5-60.08627.166643506799.9
6-100.04437.1712045564100
100.03344.817659159997.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
XDSdata scaling
XDSdata reduction
SHELXSphasing
RefinementMethod to determine structure: MIR / Resolution: 3.1→29.9 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.313 2440 4.9 %
Rwork0.275 --
obs-48858 97.8 %
Solvent computationBsol: 59.641 Å2
Displacement parametersBiso max: 200.77 Å2 / Biso mean: 119.898 Å2 / Biso min: 19.82 Å2
Baniso -1Baniso -2Baniso -3
1--30.749 Å20 Å20 Å2
2--23.186 Å20 Å2
3---7.563 Å2
Refinement stepCycle: LAST / Resolution: 3.1→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12872 0 4 0 12876
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.606
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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