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- PDB-3wyg: Crystal structure of Xpo1p-PKI-Gsp1p-GTP complex -

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Basic information

Entry
Database: PDB / ID: 3wyg
TitleCrystal structure of Xpo1p-PKI-Gsp1p-GTP complex
Components
  • Exportin-1
  • Gsp1p
  • cAMP-dependent protein kinase inhibitor alpha
KeywordsGTP-BINDING PROTEIN/GTP-BINDING PROTEIN INHIBITOR / HEAT REPEAT / NUCLEAR EXPORT / GTP-BINDING PROTEIN-GTP-BINDING PROTEIN INHIBITOR COMPLEX
Function / homology
Function and homology information


regulation of cell cycle phase transition / regulation of nucleocytoplasmic transport / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Postmitotic nuclear pore complex (NPC) reformation / negative regulation of cAMP-dependent protein kinase activity / tRNA re-export from nucleus / nuclear export signal receptor activity / Transcriptional and post-translational regulation of MITF-M expression and activity / tRNA export from nucleus / protein localization to kinetochore ...regulation of cell cycle phase transition / regulation of nucleocytoplasmic transport / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Postmitotic nuclear pore complex (NPC) reformation / negative regulation of cAMP-dependent protein kinase activity / tRNA re-export from nucleus / nuclear export signal receptor activity / Transcriptional and post-translational regulation of MITF-M expression and activity / tRNA export from nucleus / protein localization to kinetochore / spindle pole body / U4 snRNA binding / nuclear export / negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / nuclear import signal receptor activity / poly(A)+ mRNA export from nucleus / negative regulation of protein import into nucleus / nucleus organization / MAPK6/MAPK4 signaling / protein kinase A catalytic subunit binding / ribosomal large subunit export from nucleus / U5 snRNA binding / U2 snRNA binding / U6 snRNA binding / mRNA export from nucleus / U1 snRNA binding / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / regulation of G2/M transition of mitotic cell cycle / protein export from nucleus / kinetochore / small GTPase binding / protein import into nucleus / GTPase activity / GTP binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / nucleus / cytoplasm / cytosol
Similarity search - Function
Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1, C-terminal / CRM1 C terminal / Exportin-1/5 ...Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1, C-terminal / CRM1 C terminal / Exportin-1/5 / Exportin-1/Importin-beta-like / Exportin 1-like protein / Ran GTPase / Small GTPase Ran-type domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / 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 / : / Exportin-1 / GTP-binding nuclear protein GSP1/CNR1 / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesSaccharomyces cerevisiae AWRI796 (yeast)
Saccharomyces cerevisiae S288c (yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsKoyama, M. / Shirai, N. / Matsuura, Y.
CitationJournal: Cell Rep / Year: 2014
Title: Structural insights into how yrb2p accelerates the assembly of the xpo1p nuclear export complex
Authors: Koyama, M. / Shirai, N. / Matsuura, Y.
History
DepositionAug 26, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: Gsp1p
C: Exportin-1
D: cAMP-dependent protein kinase inhibitor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,6415
Polymers149,0943
Non-polymers5472
Water13,187732
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7550 Å2
ΔGint-36 kcal/mol
Surface area48500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.250, 114.680, 141.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 3 molecules ACD

#1: Protein Gsp1p


Mass: 20672.861 Da / Num. of mol.: 1 / Fragment: UNP residues 1-182 / Mutation: Q71L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae AWRI796 (yeast)
Strain: AWRI796 / Gene: AWRI796_3356 / Plasmid: PGEX-TEV / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: E7KFU1, UniProt: P32835*PLUS
#2: Protein Exportin-1 / Chromosome region maintenance protein 1 / Karyopherin-124


Mass: 120398.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288C / Gene: CRM1, G8514, KAP124, XPO1, YGR218W / Plasmid: PGEX-TEV / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P30822
#3: Protein cAMP-dependent protein kinase inhibitor alpha / PKI-alpha / cAMP-dependent protein kinase inhibitor / muscle/brain isoform


Mass: 8022.581 Da / Num. of mol.: 1 / Mutation: S35L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKIA, PRKACN1 / Plasmid: PGEX-TEV / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P61925

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Non-polymers , 3 types, 734 molecules

#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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 732 / 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: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal growpH: 7.7
Details: 0.1M TRIS, 15% PEG20000, PH 7.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 28, 2012
RadiationMonochromator: ROTATED-INCLINED DOUBLE-CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→37.75 Å / Num. obs: 95343 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.1 %
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 4.8 % / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M1I

3m1i


Resolution: 2.15→37.75 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.448 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22 4808 5 %RANDOM
Rwork0.175 ---
obs0.177 90454 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.04 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.51 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.15→37.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9603 0 33 732 10368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0199825
X-RAY DIFFRACTIONr_bond_other_d0.0010.029540
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.96213318
X-RAY DIFFRACTIONr_angle_other_deg0.854321923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.97651188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45925452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.833151786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5841542
X-RAY DIFFRACTIONr_chiral_restr0.0980.21544
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210952
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022238
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 335 -
Rwork0.273 6541 -
obs--98.86 %

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