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- PDB-4uad: Importin alpha 7 delta IBB in complex with Influenza PB2 Nuclear ... -

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Basic information

Entry
Database: PDB / ID: 4uad
TitleImportin alpha 7 delta IBB in complex with Influenza PB2 Nuclear Localization Domain
Components
  • Importin subunit alpha-7
  • Polymerase basic protein 2
KeywordsPROTEIN TRANSPORT / importin karyopherin complex NLS
Function / homology
Function and homology information


entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / positive regulation of cytokine production involved in inflammatory response / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion ...entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / positive regulation of cytokine production involved in inflammatory response / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / maternal process involved in female pregnancy / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / Assembly of the ORC complex at the origin of replication / viral genome replication / virion component / protein import into nucleus / host cell / transcription by RNA polymerase II / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
Polymerase Basic Protein 2, C-terminal domain / Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / : / : ...Polymerase Basic Protein 2, C-terminal domain / Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / : / : / : / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / Influenza RNA polymerase PB2 middle domain / Influenza RNA polymerase PB2 6th domain / Influenza RNA polymerase PB2 C-terminal domain / : / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Influenza RNA polymerase PB2 CAP binding domain / : / Influenza RNA polymerase PB2 helical domain / Defensin A-like / Armadillo/plakoglobin ARM repeat profile. / 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 / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Importin subunit alpha-7 / Polymerase basic protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.42 Å
AuthorsPumroy, R.A. / Cingolani, G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM074846 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100888 United States
CitationJournal: Structure / Year: 2015
Title: Molecular Determinants for Nuclear Import of Influenza A PB2 by Importin alpha Isoforms 3 and 7.
Authors: Pumroy, R.A. / Ke, S. / Hart, D.J. / Zachariae, U. / Cingolani, G.
History
DepositionAug 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
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 subunit alpha-7
E: Polymerase basic protein 2


Theoretical massNumber of molelcules
Total (without water)61,3632
Polymers61,3632
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)242.315, 38.836, 67.898
Angle α, β, γ (deg.)90.00, 98.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Importin subunit alpha-7 / Karyopherin subunit alpha-6


Mass: 52978.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNA6, IPOA7 / Plasmid: pTAR010 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: O60684
#2: Protein Polymerase basic protein 2 / RNA-directed RNA polymerase subunit P3


Mass: 8384.718 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Victoria/3/1975 H3N2 / Gene: PB2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: P31345
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium acetate 12% PEG 8000 0.1M Na cacodylate at pH 6.5
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.972 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.42→15 Å / Num. obs: 21920 / % possible obs: 90 % / Redundancy: 3.5 % / Net I/σ(I): 24.9
Reflection shellResolution: 2.42→2.51 Å / % possible all: 60.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementResolution: 2.42→14.86 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 23.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1998 9.12 %Random selection
Rwork0.1889 ---
obs0.1928 21910 89.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.42→14.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3867 0 0 157 4024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033925
X-RAY DIFFRACTIONf_angle_d0.7195322
X-RAY DIFFRACTIONf_dihedral_angle_d11.6731469
X-RAY DIFFRACTIONf_chiral_restr0.024633
X-RAY DIFFRACTIONf_plane_restr0.004685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.47660.3048850.2555848X-RAY DIFFRACTION55
2.4766-2.54320.28311080.24051076X-RAY DIFFRACTION68
2.5432-2.61770.25831310.22671302X-RAY DIFFRACTION82
2.6177-2.70170.3021500.23081499X-RAY DIFFRACTION96
2.7017-2.79760.2851500.22331500X-RAY DIFFRACTION93
2.7976-2.90890.25771440.22151430X-RAY DIFFRACTION94
2.9089-3.04020.27171490.20791482X-RAY DIFFRACTION93
3.0402-3.1990.23241470.21021478X-RAY DIFFRACTION93
3.199-3.39710.23311430.20651429X-RAY DIFFRACTION91
3.3971-3.65580.22181500.18781486X-RAY DIFFRACTION94
3.6558-4.01710.21931550.17631547X-RAY DIFFRACTION97
4.0171-4.58340.21191600.16221592X-RAY DIFFRACTION99
4.5834-5.71930.21171610.17641612X-RAY DIFFRACTION99
5.7193-14.85990.18261650.14441631X-RAY DIFFRACTION98

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