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- PDB-1o6o: Importin Beta aa1-442 bound to five FxFG repeats from yeast Nsp1p... -

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Basic information

Entry
Database: PDB / ID: 1o6o
TitleImportin Beta aa1-442 bound to five FxFG repeats from yeast Nsp1p. Second crystal form
Components
  • IMPORTIN BETA-1 SUBUNIT
  • NUCLEOPORIN NSP1
KeywordsNUCLEAR TRANSPORT / NUCLEAR TRAFFICKING / NUCLEOPORIN / TRANSPORT FACTOR / PROTEIN TRANSPORT
Function / homology
Function and homology information


RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / nuclear pore central transport channel / astral microtubule organization / Transport of Mature mRNA derived from an Intron-Containing Transcript / establishment of mitotic spindle localization / Regulation of HSF1-mediated heat shock response / nuclear pore nuclear basket ...RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / nuclear pore central transport channel / astral microtubule organization / Transport of Mature mRNA derived from an Intron-Containing Transcript / establishment of mitotic spindle localization / Regulation of HSF1-mediated heat shock response / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / tRNA export from nucleus / importin-alpha family protein binding / SUMOylation of SUMOylation proteins / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / NLS-bearing protein import into nucleus / Apoptosis induced DNA fragmentation / nuclear localization sequence binding / structural constituent of nuclear pore / ribosomal protein import into nucleus / Initiation of Nuclear Envelope (NE) Reformation / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / RNA export from nucleus / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of chromatin organization proteins / nuclear import signal receptor activity / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / mitotic metaphase chromosome alignment / ribosomal large subunit export from nucleus / mitotic spindle assembly / nuclear pore / ribosomal small subunit export from nucleus / nuclear periphery / Assembly of the ORC complex at the origin of replication / Hsp90 protein binding / positive regulation of cholesterol biosynthetic process / phospholipid binding / small GTPase binding / ISG15 antiviral mechanism / specific granule lumen / cytoplasmic stress granule / protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / nuclear envelope / nuclear membrane / ficolin-1-rich granule lumen / protein domain specific binding / Neutrophil degranulation / enzyme binding / RNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Nucleoporin, NSP1-like, C-terminal / Nucleoporin NSP1/NUP62 / Nsp1-like C-terminal region / Importin beta family / HEAT-like repeat / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / HEAT repeat profile. ...Nucleoporin, NSP1-like, C-terminal / Nucleoporin NSP1/NUP62 / Nsp1-like C-terminal region / Importin beta family / HEAT-like repeat / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / HEAT repeat profile. / HEAT, type 2 / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Nucleoporin NSP1 / Importin subunit beta-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBayliss, R. / Stewart, M.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Glfg and Fxfg Nucleoporins Bind to Overlapping Sites on Importin-Beta
Authors: Bayliss, R. / Littlewood, T. / Strawn, L.A. / Wente, S.R. / Stewart, M.
History
DepositionOct 10, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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: IMPORTIN BETA-1 SUBUNIT
B: IMPORTIN BETA-1 SUBUNIT
C: IMPORTIN BETA-1 SUBUNIT
D: NUCLEOPORIN NSP1
E: NUCLEOPORIN NSP1
F: NUCLEOPORIN NSP1


Theoretical massNumber of molelcules
Total (without water)185,8166
Polymers185,8166
Non-polymers00
Water23413
1
A: IMPORTIN BETA-1 SUBUNIT
D: NUCLEOPORIN NSP1


Theoretical massNumber of molelcules
Total (without water)61,9392
Polymers61,9392
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: IMPORTIN BETA-1 SUBUNIT
F: NUCLEOPORIN NSP1


Theoretical massNumber of molelcules
Total (without water)61,9392
Polymers61,9392
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: IMPORTIN BETA-1 SUBUNIT
E: NUCLEOPORIN NSP1


Theoretical massNumber of molelcules
Total (without water)61,9392
Polymers61,9392
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.110, 125.350, 266.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein IMPORTIN BETA-1 SUBUNIT / KARYOPHERIN BETA-1 SUBUNIT / NUCLEAR FACTOR P97 / IMPORTIN 90 / KPNB1 / NTF97


Mass: 49385.203 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-442
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q14974
#2: Protein NUCLEOPORIN NSP1 / NUCLEAR PORE PROTEIN NSP1 / NUCLEOSKELETAL-LIKE PROTEIN / P110 / NSP1 / YJL041W / J1207


Mass: 12553.628 Da / Num. of mol.: 3 / Fragment: RESIDUES 497-608
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14907
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIMPORTIN BETA-1 ROLE IN NUCLEAR PROTEIN IMPORT, RECEPTOR FOR NUCLEAR LOCALIZATION SIGNALS. MEMBER ...IMPORTIN BETA-1 ROLE IN NUCLEAR PROTEIN IMPORT, RECEPTOR FOR NUCLEAR LOCALIZATION SIGNALS. MEMBER OF THE IMPORTIN BETA FAMILY. CONTAINS EIGHT HEAT REPEATS. NUCLEOPORIN NSP1 POSSIBLE ROLE IN NUCLEAR OR CELL DIVISION. MAY ALSO PLAY A ROLEIN BINDING AND TRANSLOCATION OF PROTEINS DURING NUCLEAR TRAFFICKING. CONTAINS PHE-X-PHE-GLY REPEAT SEQUENCES

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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: 3.02 Å3/Da / Density % sol: 59.25 %
Crystal growpH: 5.9
Details: 1.2-1.28M AMMONIUM SULPHATE, 100MM AMMONIUM ACETATE, PH 5.9, 30MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.8→60.9 Å / Num. obs: 53288 / % possible obs: 94.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 5.5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 1.7 / % possible all: 88.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QGK

1qgk


Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 -5 %RANDOM
Rwork0.236 ---
obs0.236 53288 94.7 %-
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10420 0 0 13 10433
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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