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- PDB-2p8q: Crystal Structure of human Importin beta bound to the Snurportin1... -

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Basic information

Entry
Database: PDB / ID: 2p8q
TitleCrystal Structure of human Importin beta bound to the Snurportin1 IBB-domain
Components
  • Importin beta-1 subunitImportin
  • Snurportin-1SPN1
KeywordsPROTEIN TRANSPORT / HEAT repeat / IBB-domain / Importin / Karyopherin / Snurportin
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 / establishment of mitotic spindle localization / astral microtubule organization / RNA cap binding / snRNA import into nucleus / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) ...RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / establishment of mitotic spindle localization / astral microtubule organization / RNA cap binding / snRNA import into nucleus / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / ribosomal protein import into nucleus / importin-alpha family protein binding / NS1 Mediated Effects on Host Pathways / Initiation of Nuclear Envelope (NE) Reformation / NLS-dependent protein nuclear import complex / Apoptosis induced DNA fragmentation / Nuclear import of Rev protein / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / mitotic metaphase chromosome alignment / mitotic spindle assembly / nuclear pore / Assembly of the ORC complex at the origin of replication / Hsp90 protein binding / ISG15 antiviral mechanism / small GTPase binding / cytoplasmic stress granule / protein import into nucleus / specific granule lumen / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / nuclear envelope / snRNP Assembly / nuclear membrane / ficolin-1-rich granule lumen / protein domain specific binding / Neutrophil degranulation / enzyme binding / RNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Snurportin-1 / Snurportin-1, N-terminal / : / Snurportin1 / Importin beta family / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain ...Snurportin-1 / Snurportin-1, N-terminal / : / Snurportin1 / Importin beta family / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Importin-alpha, importin-beta-binding domain / IBB domain profile. / 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
Snurportin-1 / Importin subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMitrousis, G. / Cingolani, G.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Molecular Basis for the Recognition of Snurportin 1 by Importin {beta}.
Authors: Mitrousis, G. / Olia, A.S. / Walker-Kopp, N. / Cingolani, G.
History
DepositionMar 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Aug 30, 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

Downloads & links

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Assembly

Deposited unit
A: Importin beta-1 subunit
B: Snurportin-1


Theoretical massNumber of molelcules
Total (without water)102,2862
Polymers102,2862
Non-polymers00
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-6 kcal/mol
Surface area40640 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.752, 97.892, 84.286
Angle α, β, γ (deg.)90.00, 90.86, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer of importin beta bound to the snurportin IBB-domain

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Components

#1: Protein Importin beta-1 subunit / Importin / Karyopherin beta-1 subunit / Nuclear factor P97 / Importin 90


Mass: 97257.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNB1, NTF97 / Plasmid: pQE-3 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q14974
#2: Protein/peptide Snurportin-1 / SPN1 / RNA U transporter 1


Mass: 5027.755 Da / Num. of mol.: 1 / Fragment: N-terminal domain (25-64) / Source method: obtained synthetically / Details: This sequence occurs naturally in Homo sapiens / References: UniProt: O95149
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 22%PEG 8000, 0.05M Sodium Chloride, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.35→40 Å / Num. all: 45955 / Num. obs: 44104 / % possible obs: 95.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 20.1
Reflection shellResolution: 2.35→2.43 Å / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2.66 / Num. unique all: 2937 / Rsym value: 0.476 / % possible all: 64.1

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Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QGK

1qgk


Resolution: 2.35→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 4360 -RANDOM
Rwork0.2268 ---
all0.23 43296 --
obs0.23 43296 98.7 %-
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.35→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7126 0 0 345 7471
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_bond_d0.006
LS refinement shellResolution: 2.35→2.37 Å
RfactorNum. reflection
Rfree0.2773 51
Rwork0.2738 -
obs-689

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