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- PDB-5v5o: Structure of NLS2K of influenza A virus nucleoprotein bound to im... -

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Basic information

Entry
Database: PDB / ID: 5v5o
TitleStructure of NLS2K of influenza A virus nucleoprotein bound to importin alpha
Components
  • Importin subunit alpha-1
  • Nucleoprotein
KeywordsVIRAL PROTEIN / Nuclear Import / NLS
Function / homology
Function and homology information


cRNA Synthesis / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus ...cRNA Synthesis / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / vRNA Synthesis / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / Transport of Ribonucleoproteins into the Host Nucleus / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / NEP/NS2 Interacts with the Cellular Export Machinery / nuclear import signal receptor activity / vRNP Assembly / Viral Messenger RNA Synthesis / nuclear localization sequence binding / NLS-bearing protein import into nucleus / helical viral capsid / host cell / Viral mRNA Translation / cytoplasmic stress granule / protein import into nucleus / histone deacetylase binding / viral penetration into host nucleus / viral nucleocapsid / nuclear membrane / DNA-binding transcription factor binding / postsynaptic density / symbiont entry into host cell / ribonucleoprotein complex / glutamatergic synapse / host cell nucleus / structural molecule activity / RNA binding / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. ...Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / 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 / Mainly Alpha
Similarity search - Domain/homology
Nucleoprotein / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.243 Å
AuthorsSankhala, R.S. / Lokareddy, R.K. / Cingolani, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM100888 United States
CitationJournal: Sci Rep / Year: 2017
Title: Synergy of two low-affinity NLSs determines the high avidity of influenza A virus nucleoprotein NP for human importin alpha isoforms.
Authors: Wu, W. / Sankhala, R.S. / Florio, T.J. / Zhou, L. / Nguyen, N.L.T. / Lokareddy, R.K. / Cingolani, G. / Pante, N.
History
DepositionMar 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 26, 2020Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rpim_I_all
Revision 1.4Oct 4, 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
C: Importin subunit alpha-1
A: Nucleoprotein
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)62,5923
Polymers62,5923
Non-polymers00
Water7,314406
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Gel-filtration chromatography and isothermal titration calorimetry.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint5 kcal/mol
Surface area18510 Å2
Unit cell
Length a, b, c (Å)78.165, 90.893, 97.086
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 subunit alpha-1 / / Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit ...Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit / PTAC58 / RAG cohort protein 1 / SRP1-alpha


Mass: 57856.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52293
#2: Protein/peptide Nucleoprotein /


Mass: 2367.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Influenza A virus / References: UniProt: P03466*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.75 Å3/Da / Density % sol: 55.35 % / Description: Rectangular blocks
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M HEPES pH 6.0, 0.6 M sodium citrate tribasic dihydrate, 10 mM b-mercaptoethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.25→15 Å / Num. obs: 32858 / % possible obs: 97.8 % / Redundancy: 3.9 % / Rpim(I) all: 0.046 / Rsym value: 0.086 / Net I/σ(I): 29.5
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.5 / Rpim(I) all: 0.41 / Rsym value: 0.71 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(dev_2481)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HUY

5huy


Resolution: 2.243→14.968 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2063 1641 5 %
Rwork0.1741 --
obs0.1757 32817 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.243→14.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3333 0 0 406 3739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023389
X-RAY DIFFRACTIONf_angle_d0.5314609
X-RAY DIFFRACTIONf_dihedral_angle_d14.7182063
X-RAY DIFFRACTIONf_chiral_restr0.037552
X-RAY DIFFRACTIONf_plane_restr0.004592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2434-2.30920.33671240.31892451X-RAY DIFFRACTION93
2.3092-2.38340.36261380.29232545X-RAY DIFFRACTION97
2.3834-2.46830.28721350.26122545X-RAY DIFFRACTION98
2.4683-2.56660.27021250.22872613X-RAY DIFFRACTION98
2.5666-2.68280.25461430.21122565X-RAY DIFFRACTION98
2.6828-2.82330.20371330.19532613X-RAY DIFFRACTION98
2.8233-2.99890.23171320.18942612X-RAY DIFFRACTION99
2.9989-3.22830.21571500.18052630X-RAY DIFFRACTION99
3.2283-3.54930.19081400.16682643X-RAY DIFFRACTION99
3.5493-4.05390.18071410.13622643X-RAY DIFFRACTION99
4.0539-5.07420.17491370.12662664X-RAY DIFFRACTION98
5.0742-14.9680.1561430.14892652X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0371-0.04340.04563.73721.30630.91840.0493-0.0457-0.08520.19250.04440.1250.1928-0.0844-0.12030.2563-0.0211-0.01940.22950.01220.19255.24591.9841-15.4506
22.1425-1.0614-1.86812.19931.44693.43160.0792-0.13550.1627-0.1278-0.0228-0.0991-0.22240.0439-0.0770.18160.0084-0.01560.17850.01670.2408-5.120130.8736-4.2003
32.4792-0.09830.38124.63240.38444.67770.1308-0.9990.25091.01560.0159-0.4445-0.05130.609-0.00890.4671-0.0369-0.03250.7482-0.15270.3922-7.801739.621523.8322
49.0833-1.99470.60684.08193.61833.9441-0.2739-0.63280.5897-0.56070.30360.83070.98480.1841-0.18951.15770.04210.12570.6642-0.02670.9283-1.84917.3931-7.1092
54.0765-0.7818-0.45370.3364-1.04026.85960.30040.1133-0.6145-0.52670.3168-0.48880.11420.1842-0.63121.0390.24460.070.9749-0.13440.83081.613232.25187.84
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 75 through 245 )
2X-RAY DIFFRACTION2chain 'C' and (resid 246 through 375 )
3X-RAY DIFFRACTION3chain 'C' and (resid 376 through 497 )
4X-RAY DIFFRACTION4chain 'A' and (resid 209 through 216 )
5X-RAY DIFFRACTION5chain 'B' and (resid 212 through 216 )

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