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- PDB-5yu7: CRYSTAL STRUCTURE OF EXPORTIN-5 -

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Basic information

Entry
Database: PDB / ID: 5yu7
TitleCRYSTAL STRUCTURE OF EXPORTIN-5
ComponentsExportin-5
KeywordsRNA BINDING PROTEIN
Function / homology
Function and homology information


RISC complex binding / pre-miRNA binding / RNA nuclear export complex / pre-miRNA export from nucleus / nuclear export signal receptor activity / miRNA metabolic process / RISC complex / RNA export from nucleus / MicroRNA (miRNA) biogenesis / protein export from nucleus ...RISC complex binding / pre-miRNA binding / RNA nuclear export complex / pre-miRNA export from nucleus / nuclear export signal receptor activity / miRNA metabolic process / RISC complex / RNA export from nucleus / MicroRNA (miRNA) biogenesis / protein export from nucleus / small GTPase binding / tRNA binding / mRNA binding / 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 / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant ...Exportin-5, C-terminal domain / Exportin-5 family / Exportin-1/5 / Exportin-1/Importin-beta-like / Exportin 1-like protein / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.301 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 1.2Jul 7, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exportin-5


Theoretical massNumber of molelcules
Total (without water)136,4551
Polymers136,4551
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area50580 Å2
Unit cell
Length a, b, c (Å)286.163, 286.163, 59.349
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

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


Mass: 136454.719 Da / Num. of mol.: 1
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

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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: 5.14 Å3/Da / Density % sol: 76.07 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / Details: PEG3350, Tacsimate, MPD, MgCl2, DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 42325 / % possible obs: 99.5 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 28
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.845 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2056 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A6P

3a6p


Resolution: 3.301→41.304 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 2156 5.1 %RANDOM
Rwork0.1996 ---
obs0.2011 42295 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.301→41.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8937 0 0 0 8937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029112
X-RAY DIFFRACTIONf_angle_d0.44212330
X-RAY DIFFRACTIONf_dihedral_angle_d9.5535582
X-RAY DIFFRACTIONf_chiral_restr0.0341420
X-RAY DIFFRACTIONf_plane_restr0.0031572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3007-3.37740.35181380.31372628X-RAY DIFFRACTION100
3.3774-3.46190.31281550.2872657X-RAY DIFFRACTION100
3.4619-3.55540.30641440.25512648X-RAY DIFFRACTION100
3.5554-3.660.26331540.23462663X-RAY DIFFRACTION100
3.66-3.7780.25171410.22242662X-RAY DIFFRACTION100
3.778-3.9130.24461420.20222684X-RAY DIFFRACTION100
3.913-4.06950.26671620.20512632X-RAY DIFFRACTION100
4.0695-4.25450.19351330.17722713X-RAY DIFFRACTION100
4.2545-4.47860.23151520.1832657X-RAY DIFFRACTION100
4.4786-4.75880.18781330.17452677X-RAY DIFFRACTION100
4.7588-5.12560.20881570.18082685X-RAY DIFFRACTION100
5.1256-5.64030.26661160.20572730X-RAY DIFFRACTION100
5.6403-6.45380.27861180.22562758X-RAY DIFFRACTION100
6.4538-8.12090.24271620.21252706X-RAY DIFFRACTION100
8.1209-41.30730.1871490.17322639X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: 121.8252 Å / Origin y: 41.236 Å / Origin z: -3.8069 Å
111213212223313233
T1.3847 Å2-0.0017 Å2-0.3483 Å2-0.7982 Å20.1041 Å2--1.0115 Å2
L2.2352 °2-1.504 °2-0.6245 °2-2.4257 °2-0.1146 °2--0.6133 °2
S-0.2062 Å °-0.0127 Å °1.0053 Å °0.1069 Å °0.4364 Å °-0.2684 Å °-0.3489 Å °-0.1843 Å °-0.2132 Å °
Refinement TLS groupSelection details: all

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