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- PDB-5v5p: Structure of NLS2R of influenza A virus nucleoprotein bound to im... -

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Basic information

Entry
Database: PDB / ID: 5v5p
TitleStructure of NLS2R 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


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 / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / helical viral capsid / viral penetration into host nucleus / cytoplasmic stress granule / protein import into nucleus ...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 / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / helical viral capsid / viral penetration into host nucleus / cytoplasmic stress granule / protein import into nucleus / host cell / viral nucleocapsid / DNA-binding transcription factor binding / postsynaptic density / ribonucleoprotein complex / host cell nucleus / glutamatergic synapse / structural molecule activity / RNA binding / nucleoplasm / 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
Importin subunit alpha-1 / Nucleoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 1.3Oct 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)62,6483
Polymers62,6483
Non-polymers00
Water4,197233
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 area1890 Å2
ΔGint3 kcal/mol
Surface area18710 Å2
Unit cell
Length a, b, c (Å)78.646, 91.322, 97.771
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 / Fragment: residues 2-529
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52293
#2: Protein/peptide Nucleoprotein


Mass: 2395.668 Da / Num. of mol.: 2 / Fragment: residues 10-28 / Source method: obtained synthetically / Details: Peptide was synthesized commercially
Source: (synth.) Influenza A virus (A/swine/Bakum/5/95(H1N1))
References: UniProt: Q45VS8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.8 Å3/Da / Density % sol: 56.11 % / Description: Rectangular blocks
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.6 M sodium citrate, 100 mM Hepes, and 10 mM beta-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: 2.15→15 Å / Num. obs: 42795 / % possible obs: 99.6 % / Redundancy: 5.6 % / Rpim(I) all: 0.039 / Rsym value: 0.084 / Net I/σ(I): 30.2
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 4.1 / Rpim(I) all: 0.32 / Rsym value: 0.69 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HUY

5huy


Resolution: 2.15→14.986 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2104 1804 4.68 %
Rwork0.1798 --
obs0.1812 38574 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→14.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3316 0 0 233 3549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033372
X-RAY DIFFRACTIONf_angle_d0.5364587
X-RAY DIFFRACTIONf_dihedral_angle_d16.6942053
X-RAY DIFFRACTIONf_chiral_restr0.037550
X-RAY DIFFRACTIONf_plane_restr0.004589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.2080.31011410.29842778X-RAY DIFFRACTION99
2.208-2.27270.32531190.27882813X-RAY DIFFRACTION99
2.2727-2.34580.29941550.24222778X-RAY DIFFRACTION99
2.3458-2.42930.26641270.22542807X-RAY DIFFRACTION100
2.4293-2.52610.25711420.20772804X-RAY DIFFRACTION100
2.5261-2.64050.25291400.19892802X-RAY DIFFRACTION99
2.6405-2.77890.21681300.18822811X-RAY DIFFRACTION100
2.7789-2.95180.19811460.18382827X-RAY DIFFRACTION99
2.9518-3.17770.21281360.1752826X-RAY DIFFRACTION99
3.1777-3.49380.22151480.17852828X-RAY DIFFRACTION100
3.4938-3.9910.18741340.15312858X-RAY DIFFRACTION99
3.991-4.99710.16621430.14442877X-RAY DIFFRACTION99
4.9971-14.98630.17421430.16172961X-RAY DIFFRACTION98
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)
10.5406-0.27880.79530.1837-0.69713.2318-0.2855-0.2418-0.718-0.2143-0.0445-0.49750.08110.2140.31170.84070.0438-0.16030.9297-0.27181.32761.33532.51238.1713
21.11060.3920.6684.0261.22430.9060.0913-0.0552-0.04720.30740.04160.06950.2145-0.0553-0.12480.2911-0.0116-0.02240.26150.00590.21566.2902-2.8615-15.1537
31.2762-0.6636-0.49722.07260.7911.91380.0608-0.0650.0712-0.1398-0.01010.0162-0.1146-0.0558-0.06370.1932-0.00290.00420.20230.01660.2376-1.206523.4373-12.0402
41.97640.0216-0.90442.71080.51712.21550.1232-0.71850.26790.43030.014-0.3169-0.06340.4582-0.06950.2724-0.0259-0.02860.4696-0.10770.3125-8.284738.839117.6183
51.85213.17132.95585.90285.53538.04640.44590.0444-0.10470.1807-0.27620.2621-0.27120.1984-0.02660.9195-0.10180.00540.7471-0.01540.5213-1.48624.7577-9.2161
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 212 through 216 )
2X-RAY DIFFRACTION2chain 'C' and (resid 75 through 202 )
3X-RAY DIFFRACTION3chain 'C' and (resid 203 through 322 )
4X-RAY DIFFRACTION4chain 'C' and (resid 323 through 497 )
5X-RAY DIFFRACTION5chain 'A' and (resid 212 through 216 )

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