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- PDB-1o6p: Importin Beta bound to a GLFG Nucleoporin peptide -

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Basic information

Entry
Database: PDB / ID: 1o6p
TitleImportin Beta bound to a GLFG Nucleoporin peptide
Components
  • IMPORTIN BETA-1 SUBUNIT
  • SYNTHETIC GLFG PEPTIDE
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 / telomere tethering at nuclear periphery / nuclear pore organization / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear pore cytoplasmic filaments ...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 / telomere tethering at nuclear periphery / nuclear pore organization / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear pore cytoplasmic filaments / establishment of mitotic spindle localization / Regulation of HSF1-mediated heat shock response / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / 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 / Initiation of Nuclear Envelope (NE) Reformation / ribosomal protein import into nucleus / 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 / mRNA export from nucleus / Assembly of the ORC complex at the origin of replication / Hsp90 protein binding / positive regulation of cholesterol biosynthetic process / 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 / ATPase binding / 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 / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Nucleoporin FG repeat / Nucleoporin FG repeat region / Importin beta family / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / HEAT-like repeat / Importin-beta N-terminal domain ...Nucleoporin FG repeat / Nucleoporin FG repeat region / Importin beta family / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / 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 NUP116/NSP116 / Importin subunit beta-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
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 1.0Apr 24, 2003Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Dec 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: SYNTHETIC GLFG PEPTIDE
D: SYNTHETIC GLFG PEPTIDE
E: SYNTHETIC GLFG PEPTIDE
F: SYNTHETIC GLFG PEPTIDE


Theoretical massNumber of molelcules
Total (without water)102,2426
Polymers102,2426
Non-polymers00
Water64936
1
A: IMPORTIN BETA-1 SUBUNIT
D: SYNTHETIC GLFG PEPTIDE
E: SYNTHETIC GLFG PEPTIDE


Theoretical massNumber of molelcules
Total (without water)51,1213
Polymers51,1213
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: IMPORTIN BETA-1 SUBUNIT
C: SYNTHETIC GLFG PEPTIDE
F: SYNTHETIC GLFG PEPTIDE


Theoretical massNumber of molelcules
Total (without water)51,1213
Polymers51,1213
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)125.820, 67.030, 129.260
Angle α, β, γ (deg.)90.00, 98.99, 90.00
Int Tables number4
Space group name H-MP1211
DetailsA TRIMERIC ASSEMBLY IS FORMED BY THE ASSOCIATIONOF TWO MOLECULES OF THE PEPTIDE BOUND TO ONE MOLECULEOF CHAINS A AND B

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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.: 2 / Fragment: IMPORTIN BETA-1 SUBUNIT, RESIDUES 1-442
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q14974
#2: Protein/peptide
SYNTHETIC GLFG PEPTIDE


Mass: 867.925 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) / References: UniProt: Q02630*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 5.27 Å3/Da / Density % sol: 77.3 %
Crystal growpH: 6
Details: 100MM AMMONIUM ACETATE PH6.0, 1.2M AMMONIUM SULPHATE, pH 6.00
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
225 mMpeptide1drop
3100 mMammonium acetate1reservoirpH6.0
41.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.8→67.4 Å / Num. obs: 48209 / % possible obs: 91.8 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 7.9
Reflection
*PLUS
Num. measured all: 257406
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.95 Å / % possible obs: 89.6 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QGR

1qgr


Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.267 -5 %RANDOM
Rwork0.238 ---
obs0.238 48209 91.8 %-
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6986 0 0 36 7022
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
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
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.269
Solvent computation
*PLUS
Displacement parameters
*PLUS

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