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- PDB-6fvb: Structure of Lph2 , a novel bidirectional nuclear transport recep... -

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Basic information

Entry
Database: PDB / ID: 6fvb
TitleStructure of Lph2 , a novel bidirectional nuclear transport receptor in S. cerevisiae
ComponentsImportin beta-like protein KAP120
KeywordsNUCLEAR PROTEIN / Nuclear transport receptor
Function / homology
Function and homology information


nuclear localization sequence binding / nuclear import signal receptor activity / small GTPase binding / protein import into nucleus / nuclear envelope / nucleus / cytosol / cytoplasm
Similarity search - Function
Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Importin beta-like protein KAP120
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.297 Å
AuthorsVera Rodriguez, A. / Huyton, T. / Gorlich, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB860 Germany
CitationJournal: To Be Published
Title: Structure of Lph2 , a novel bidirectional nuclear transport receptor in S. cerevisiae
Authors: Vera Rodriguez, A. / Huyton, T. / Gorlich, D.
History
DepositionMar 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Importin beta-like protein KAP120


Theoretical massNumber of molelcules
Total (without water)120,4521
Polymers120,4521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area46270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.851, 139.851, 148.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Importin beta-like protein KAP120 / Karyopherin-120


Mass: 120452.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: KAP120, YPL125W / Production host: Escherichia coli (E. coli) / References: UniProt: Q02932
Has protein modificationY

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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: 3.03 Å3/Da / Density % sol: 59.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 10% MPD 100mm MES pH6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97797 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97797 Å / Relative weight: 1
ReflectionResolution: 3.298→49.44 Å / Num. obs: 22733 / % possible obs: 99.89 % / Redundancy: 26.2 % / Net I/σ(I): 23.94
Reflection shellResolution: 3.298→3.416 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_2873: ???)refinement
XDSdata reduction
XDSdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 3.297→49.445 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2823 2129 5.04 %
Rwork0.2372 --
obs0.2395 42266 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.297→49.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8189 0 0 0 8189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2966-3.37330.4181410.42722588X-RAY DIFFRACTION98
3.3733-3.45760.29351450.36792697X-RAY DIFFRACTION100
3.4576-3.55110.3381420.32952667X-RAY DIFFRACTION100
3.5511-3.65560.31751420.30692668X-RAY DIFFRACTION100
3.6556-3.77350.29451460.28952719X-RAY DIFFRACTION100
3.7735-3.90830.34711390.27312680X-RAY DIFFRACTION100
3.9083-4.06470.27241410.27312667X-RAY DIFFRACTION100
4.0647-4.24960.28821450.26362669X-RAY DIFFRACTION100
4.2496-4.47360.28561430.23992686X-RAY DIFFRACTION100
4.4736-4.75360.23241420.22332689X-RAY DIFFRACTION100
4.7536-5.12030.32611420.22112680X-RAY DIFFRACTION100
5.1203-5.63490.32661370.26672696X-RAY DIFFRACTION100
5.6349-6.44880.27161370.2692662X-RAY DIFFRACTION100
6.4488-8.1190.31641450.24292694X-RAY DIFFRACTION100
8.119-49.45030.23551420.17352675X-RAY DIFFRACTION100

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