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- PDB-3icq: Karyopherin nuclear state -

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Basic information

Entry
Database: PDB / ID: 3icq
TitleKaryopherin nuclear state
Components
  • Exportin-T
  • GTP-binding nuclear protein GSP1/CNR1
  • RNA (62-MER)
KeywordsRNA BINDING PROTEIN / karyopherin / exportin / HEAT repeat / tRNA / GTPase
Function / homology
Function and homology information


tRNA re-export from nucleus / regulation of cell cycle phase transition / Postmitotic nuclear pore complex (NPC) reformation / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of nucleocytoplasmic transport / tRNA export from nucleus / nuclear export signal receptor activity / poly(A)+ mRNA export from nucleus / nucleus organization / tRNA processing ...tRNA re-export from nucleus / regulation of cell cycle phase transition / Postmitotic nuclear pore complex (NPC) reformation / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of nucleocytoplasmic transport / tRNA export from nucleus / nuclear export signal receptor activity / poly(A)+ mRNA export from nucleus / nucleus organization / tRNA processing / ribosomal subunit export from nucleus / nuclear pore / small GTPase binding / nuclear matrix / protein import into nucleus / nuclear envelope / tRNA binding / GTPase activity / 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 / 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 ...Exportin-T / Exportin-T, C-terminal domain / Exportin-T / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / Exportin-T / GTP-binding nuclear protein GSP1/CNR1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 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 18, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq / 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_conn.pdbx_dist_value / _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.ptnr2_label_seq_id / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: Exportin-T
B: GTP-binding nuclear protein GSP1/CNR1
D: RNA (62-MER)
U: Exportin-T
C: GTP-binding nuclear protein GSP1/CNR1
E: RNA (62-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,35010
Polymers303,2556
Non-polymers1,0954
Water724
1
T: Exportin-T
B: GTP-binding nuclear protein GSP1/CNR1
D: RNA (62-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,1755
Polymers151,6273
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-48 kcal/mol
Surface area56750 Å2
MethodPISA
2
U: Exportin-T
C: GTP-binding nuclear protein GSP1/CNR1
E: RNA (62-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,1755
Polymers151,6273
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-48 kcal/mol
Surface area56160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.000, 143.800, 166.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules TUBC

#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: Protein GTP-binding nuclear protein GSP1/CNR1 / GTPase Ran homolog / Genetic suppressor of PRP20-1 / Chromosome stability protein 17


Mass: 19717.814 Da / Num. of mol.: 2 / Fragment: Ran, UNP residues 9-179 / Mutation: Q71L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CNR1, CST17, GSP1, L8003.19, YLR293C / Plasmid: pProEX-Htb / Production host: Escherichia coli (E. coli) / Strain (production host): DL-41 / References: UniProt: P32835

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RNA chain , 1 types, 2 molecules DE

#3: RNA chain RNA (62-MER)


Mass: 21554.781 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Nucleotide synthesis

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Non-polymers , 3 types, 8 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.83 Å3/Da / Density % sol: 56.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100mM Bis-Tris, pH5.5, 20% PEG3350, 180mM sodium acetate at 18 degrees, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1Bis-TrisBis-tris methane11
2PEG335011
3sodium acetate11
4HOH11
5Bis-TrisBis-tris methane12
6PEG335012
7sodium acetate12
8HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.07 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 26, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 3.2→72.174 Å / Num. all: 57452 / Num. obs: 57452 / % possible obs: 100 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.149 / Rsym value: 0.149 / Net I/σ(I): 10.1
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.6 / Num. measured all: 34787 / Num. unique all: 8276 / Rsym value: 0.65 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 51.1 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.2 Å59.95 Å
Translation3.2 Å59.95 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASER2.1.3phasing
CNSrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3IBV

3ibv


Resolution: 3.2→50 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.771 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.294 2914 5.1 %random
Rwork0.243 ---
all-57460 --
obs-57375 100 %-
Solvent computationBsol: 50.59 Å2
Displacement parametersBiso max: 201.92 Å2 / Biso mean: 72.103 Å2 / Biso min: 2.92 Å2
Baniso -1Baniso -2Baniso -3
1-7.151 Å20 Å20 Å2
2---0.586 Å20 Å2
3----6.564 Å2
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16422 2633 66 4 19125
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.407
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4GTP.param
X-RAY DIFFRACTION5water_rep.param

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