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- PDB-5yu6: CRYSTAL STRUCTURE OF EXPORTIN-5:RANGTP COMPLEX -

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Basic information

Entry
Database: PDB / ID: 5yu6
TitleCRYSTAL STRUCTURE OF EXPORTIN-5:RANGTP COMPLEX
Components
  • 13-mer peptide
  • Exportin-5
  • GTP-binding nuclear protein Ran
KeywordsRNA BINDING PROTEIN/NUCLEAR PROTEIN / RNA BINDING PROTEIN-NUCLEAR PROTEIN COMPLEX
Function / homology
Function and homology information


RISC complex binding / pre-miRNA binding / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / nuclear export signal receptor activity / miRNA metabolic process / RISC complex / RNA export from nucleus / GTP metabolic process ...RISC complex binding / pre-miRNA binding / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / nuclear export signal receptor activity / miRNA metabolic process / RISC complex / RNA export from nucleus / GTP metabolic process / MicroRNA (miRNA) biogenesis / mitotic sister chromatid segregation / ribosomal subunit export from nucleus / protein export from nucleus / positive regulation of protein export from nucleus / small GTPase binding / protein import into nucleus / nuclear envelope / melanosome / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / tRNA binding / cell division / GTPase activity / mRNA binding / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Exportin-5, C-terminal domain / Exportin-5 family / 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 ...Exportin-5, C-terminal domain / Exportin-5 family / 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 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / 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 / Alpha Horseshoe / 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 / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / GTP-binding nuclear protein Ran / Exportin-5
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
Canis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.997 Å
AuthorsYamazawa, R. / Jiko, C. / Lee, S.J. / Yamashita, E.
Funding support Japan, Korea, Republic Of, 4items
OrganizationGrant numberCountry
MEXT22121006 Japan
JSPS22370041 Japan
JSPS21227003 Japan
NRFMEST 2011-0017405 Korea, Republic Of
CitationJournal: Structure / Year: 2018
Title: Structural Basis for Selective Binding of Export Cargoes by Exportin-5
Authors: Yamazawa, R. / Jiko, C. / Choi, S. / Park, I.Y. / Nakagawa, A. / Yamashita, E. / Lee, S.J.
History
DepositionNov 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 25, 2019Group: Derived calculations / Category: pdbx_struct_assembly_gen / Item: _pdbx_struct_assembly_gen.asym_id_list
Revision 1.3Nov 22, 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 / struct_conn
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_label_asym_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exportin-5
E: 13-mer peptide
B: GTP-binding nuclear protein Ran
C: Exportin-5
F: 13-mer peptide
D: GTP-binding nuclear protein Ran
hetero molecules


Theoretical massNumber of molelcules
Total (without water)325,16510
Polymers324,0706
Non-polymers1,0954
Water00
1
A: Exportin-5
E: 13-mer peptide
B: GTP-binding nuclear protein Ran
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,5835
Polymers162,0353
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Exportin-5
F: 13-mer peptide
D: GTP-binding nuclear protein Ran
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,5835
Polymers162,0353
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.560, 302.678, 88.264
Angle α, β, γ (deg.)90.00, 109.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Exportin-5 / Exp5 / Ran-binding protein 21


Mass: 136454.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XPO5, KIAA1291, RANBP21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HAV4
#2: Protein/peptide 13-mer peptide


Mass: 1124.378 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)
#3: Protein GTP-binding nuclear protein Ran / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear protein


Mass: 24456.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: RAN / Production host: Escherichia coli (E. coli) / References: UniProt: P62825
#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
Has protein modificationY
Sequence detailsREGARDING THE RESIDUES AT POSITION 1305-1317 (CHAINS E/F), THE AUTHORS DO NOT KNOW EACH SEQUENCE. ...REGARDING THE RESIDUES AT POSITION 1305-1317 (CHAINS E/F), THE AUTHORS DO NOT KNOW EACH SEQUENCE. IN ADDITION, THEY COULDN'T SPECIFY ALL OF THE AMINO ACIDS DUE TO THE DISCONTINUOUS ELECTRON DENSITY.

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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: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350, DTT, MgCl2, spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: IMAGE PLATE / Date: Feb 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3→83.33 Å / Num. obs: 55602 / % possible obs: 82.3 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5227 / % possible all: 77.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A6P

3a6p


Resolution: 2.997→48.977 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 28.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2689 2871 5.17 %RANDOM
Rwork0.2183 ---
obs0.2209 55507 81.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.997→48.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20030 0 66 0 20096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00220503
X-RAY DIFFRACTIONf_angle_d0.50627769
X-RAY DIFFRACTIONf_dihedral_angle_d14.33312471
X-RAY DIFFRACTIONf_chiral_restr0.0373182
X-RAY DIFFRACTIONf_plane_restr0.0043521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9969-3.0460.36251310.28352172X-RAY DIFFRACTION72
3.046-3.09850.35541530.28562331X-RAY DIFFRACTION77
3.0985-3.15480.32821160.27652383X-RAY DIFFRACTION78
3.1548-3.21550.35731380.28712341X-RAY DIFFRACTION78
3.2155-3.28110.34251290.27852383X-RAY DIFFRACTION76
3.2811-3.35250.31041220.25662356X-RAY DIFFRACTION79
3.3525-3.43040.27671350.24422330X-RAY DIFFRACTION75
3.4304-3.51620.29491410.24332311X-RAY DIFFRACTION78
3.5162-3.61120.31751340.2492334X-RAY DIFFRACTION75
3.6112-3.71750.33331180.23952349X-RAY DIFFRACTION77
3.7175-3.83740.26331330.23082313X-RAY DIFFRACTION75
3.8374-3.97450.26851140.22212351X-RAY DIFFRACTION77
3.9745-4.13360.27381450.20372329X-RAY DIFFRACTION77
4.1336-4.32160.2441300.19532390X-RAY DIFFRACTION78
4.3216-4.54930.23841250.19282474X-RAY DIFFRACTION80
4.5493-4.83410.20721370.18452589X-RAY DIFFRACTION85
4.8341-5.20690.22441420.19732844X-RAY DIFFRACTION92
5.2069-5.73020.26911640.21852951X-RAY DIFFRACTION96
5.7302-6.55770.28991600.23183002X-RAY DIFFRACTION99
6.5577-8.25560.25451540.21673069X-RAY DIFFRACTION99
8.2556-48.98330.21511500.17283034X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 33.9016 Å / Origin y: 60.0422 Å / Origin z: 26.4587 Å
111213212223313233
T0.2394 Å2-0.0232 Å2-0.1363 Å2-0.2638 Å20.0413 Å2--0.3263 Å2
L-0.0964 °2-0.0396 °2-0.1172 °2-0.273 °2-0.0412 °2--0.0742 °2
S-0.0191 Å °0.0273 Å °-0.0036 Å °0.0609 Å °0.0529 Å °-0.069 Å °0.0268 Å °0.025 Å °0.0153 Å °
Refinement TLS groupSelection details: all

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