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- PDB-3wyf: Crystal structure of Xpo1p-Yrb2p-Gsp1p-GTP complex -

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Basic information

Entry
Database: PDB / ID: 3wyf
TitleCrystal structure of Xpo1p-Yrb2p-Gsp1p-GTP complex
Components
  • Exportin-1
  • Gsp1p
  • Ran-specific GTPase-activating protein 2
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


tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / Transcriptional and post-translational regulation of MITF-M expression and activity / Regulation of HSF1-mediated heat shock response / nuclear export signal receptor activity / tRNA export from nucleus / SUMOylation of SUMOylation proteins / protein localization to kinetochore / NLS-bearing protein import into nucleus / SUMOylation of RNA binding proteins ...tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / Transcriptional and post-translational regulation of MITF-M expression and activity / Regulation of HSF1-mediated heat shock response / nuclear export signal receptor activity / tRNA export from nucleus / SUMOylation of SUMOylation proteins / protein localization to kinetochore / NLS-bearing protein import into nucleus / SUMOylation of RNA binding proteins / U4 snRNA binding / spindle pole body / nuclear export / SUMOylation of chromatin organization proteins / nuclear import signal receptor activity / MAPK6/MAPK4 signaling / ribosomal large subunit export from nucleus / U5 snRNA binding / U2 snRNA binding / U6 snRNA binding / mRNA export from nucleus / U1 snRNA binding / ribosomal small subunit export from nucleus / GTPase activator activity / protein export from nucleus / small GTPase binding / kinetochore / perinuclear region of cytoplasm / nucleus / cytosol / cytoplasm
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 binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Armadillo-like helical / Alpha Horseshoe / PH-like domain superfamily / Armadillo-type fold / Roll / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / : / Exportin-1 / Ran-specific GTPase-activating protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae AWRI796 (yeast)
Saccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 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_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_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
B: Ran-specific GTPase-activating protein 2
C: Exportin-1
D: Gsp1p
E: Ran-specific GTPase-activating protein 2
F: Exportin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)344,01710
Polymers342,9226
Non-polymers1,0954
Water15,997888
1
A: Gsp1p
B: Ran-specific GTPase-activating protein 2
C: Exportin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,0095
Polymers171,4613
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11390 Å2
ΔGint-65 kcal/mol
Surface area57630 Å2
MethodPISA
2
D: Gsp1p
E: Ran-specific GTPase-activating protein 2
F: Exportin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,0095
Polymers171,4613
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10870 Å2
ΔGint-58 kcal/mol
Surface area55310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.490, 155.950, 149.820
Angle α, β, γ (deg.)90.00, 106.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 6 molecules ADBECF

#1: Protein Gsp1p


Mass: 24825.357 Da / Num. of mol.: 2 / 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
#2: Protein Ran-specific GTPase-activating protein 2 / Ran-binding protein 2 / RANBP2


Mass: 26237.648 Da / Num. of mol.: 2 / Fragment: UNP residues 90-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: AWRI796_2363, YIL063C, YRB2 / Plasmid: PET30A-TEV / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P40517
#3: Protein Exportin-1 / Chromosome region maintenance protein 1 / Karyopherin-124


Mass: 120398.195 Da / Num. of mol.: 2
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: PET30A-TEV / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P30822

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Non-polymers , 3 types, 892 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-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


Mass: 18.015 Da / Num. of mol.: 888 / 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: 2.85 Å3/Da / Density % sol: 56.87 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.7
Details: 0.1M CITRATE, 17% PEG6000, PH 5.7, 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 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 6, 2011
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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.776
11H, -K, -H-L20.224
ReflectionResolution: 2.22→33.69 Å / Num. obs: 187333 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.6 %
Reflection shellResolution: 2.22→2.26 Å / Redundancy: 2.6 % / % possible all: 90.6

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Processing

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

3m1i


Resolution: 2.22→33.69 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.407 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.214 9474 5.1 %RANDOM
Rwork0.175 ---
obs0.177 177820 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.06 Å2
Baniso -1Baniso -2Baniso -3
1-12.4 Å20 Å213.46 Å2
2--0.99 Å20 Å2
3----13.39 Å2
Refinement stepCycle: LAST / Resolution: 2.22→33.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21466 0 66 888 22420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01921940
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.96129737
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64252681
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.35225.036985
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.184153890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3771587
X-RAY DIFFRACTIONr_chiral_restr0.120.23460
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02116180
X-RAY DIFFRACTIONr_gen_planes_other
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: 2.22→2.27 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 637 -
Rwork0.235 11706 -
obs--87.76 %

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