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- PDB-4zdu: Crystal structure of importin-alpha bound to a non-classical nucl... -

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Basic information

Entry
Database: PDB / ID: 4zdu
TitleCrystal structure of importin-alpha bound to a non-classical nuclear localization signal of the influenza A virus nucleoprotein
Components
  • Importin subunit alpha-1
  • Peptide from Nucleoprotein
KeywordsPROTEIN TRANSPORT/SIGNALING PROTEIN / importin / NLS / PROTEIN TRANSPORT-SIGNALING PROTEIN complex
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 / helical viral capsid / NLS-bearing protein import into nucleus / Viral mRNA Translation / cytoplasmic stress granule / viral penetration into host nucleus / protein import into nucleus / host cell / viral nucleocapsid / DNA-binding transcription factor binding / postsynaptic density / ribonucleoprotein complex / symbiont entry into host cell / 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 / molecular replacement / Resolution: 2.3 Å
AuthorsNakada, R. / Hirano, H. / Matsuura, Y.
CitationJournal: Sci Rep / Year: 2015
Title: Structure of importin-alpha bound to a non-classical nuclear localization signal of the influenza A virus nucleoprotein
Authors: Nakada, R. / Hirano, H. / Matsuura, Y.
History
DepositionApr 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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 subunit alpha-1
B: Peptide from Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)48,1362
Polymers48,1362
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint1 kcal/mol
Surface area18150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.250, 110.250, 204.361
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-531-

HOH

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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: 46374.152 Da / Num. of mol.: 1 / Fragment: UNP residues 72-498
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P52293
#2: Protein/peptide Peptide from Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 1761.866 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Strain: A/Puerto Rico/8/1934 H1N1 / Gene: NP / Plasmid: pGEX-TEV / Production host: Escherichia coli (E. coli) / References: UniProt: P03466
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.49 Å3/Da / Density % sol: 50.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→31.83 Å / Num. obs: 21538 / % possible obs: 100 % / Redundancy: 9.2 % / Biso Wilson estimate: 38.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.034 / Net I/σ(I): 14.4 / Num. measured all: 197452 / Scaling rejects: 274
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.3-2.389.50.8023.31966720700.9550.274100
8.91-31.838.70.0340.935604110.9990.0197.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata collection
Aimless0.3.11data scaling
MOLREPphasing
PDB_EXTRACT3.15data extraction
Aimlessdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UL1

3ul1


Resolution: 2.3→31.826 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2458 1066 4.96 %
Rwork0.1882 20412 -
obs0.191 21478 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.48 Å2 / Biso mean: 52.5505 Å2 / Biso min: 24.43 Å2
Refinement stepCycle: final / Resolution: 2.3→31.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 0 0 80 3332
Biso mean---51.06 -
Num. residues----428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033308
X-RAY DIFFRACTIONf_angle_d0.8084505
X-RAY DIFFRACTIONf_chiral_restr0.026545
X-RAY DIFFRACTIONf_plane_restr0.004575
X-RAY DIFFRACTIONf_dihedral_angle_d13.1751200
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.40460.33081260.25492503262999
2.4046-2.53140.27091220.23512516263899
2.5314-2.68990.28431300.216425312661100
2.6899-2.89740.29141150.218925462661100
2.8974-3.18880.24811480.205525262674100
3.1888-3.64960.23871400.198825362676100
3.6496-4.59590.23681560.160125622718100
4.5959-31.82950.21731290.165626922821100
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)
14.30050.07890.4293.3669-1.47451.05-0.5978-1.4464-0.29191.21130.2393-0.6051.00732.03810.33350.7840.4285-0.09231.0649-0.00280.514934.471237.3639.8308
21.7311.5505-0.04143.0727-0.89943.6283-0.603-0.4261-0.27340.17590.3897-0.21280.78051.14450.14020.58120.42930.08740.55920.04860.399628.976830.852528.0219
33.12130.0075-0.31574.07291.48034.0088-0.2082-0.0958-0.37220.42310.25940.14230.65740.2234-0.07490.43580.06580.00370.26170.02830.283324.743926.74589.3354
42.1116-1.5574-1.74185.06992.48564.78550.0618-0.00290.06810.03340.012-0.0647-0.1233-0.1131-0.09020.2566-0.0164-0.04130.24830.01820.280232.923817.3399-8.7095
52.7478-2.3736-0.42513.6636-2.14524.6483-0.1857-0.1869-0.12410.30580.0902-0.3092-0.04510.10260.05270.36670.0156-0.03130.291-0.05250.361843.33464.9461-14.4729
62.1010.2611-0.10979.16962.5252.34510.41641.13660.2427-1.3597-0.60110.3557-0.5484-0.45070.05170.59090.1271-0.09220.40580.02150.311839.34893.0942-28.4947
71.654-0.85960.25143.0737-0.56586.77660.1177-0.12650.0090.05610.11220.24691.1255-0.256-0.21650.4339-0.0892-0.02840.250.04050.379745.0729-4.5603-16.3867
83.35380.24395.05294.72990.60777.69810.17050.4081-0.7828-0.528-0.0547-0.1590.9059-0.0655-0.10310.5954-0.0832-0.03320.4189-0.03020.466646.0344-8.4791-29.8182
95.9870.8406-3.58125.8003-1.75958.4919-0.4859-0.6059-0.7747-0.1310.08610.21581.58610.17630.36550.75720.0163-0.020.4340.06090.541249.5817-14.6125-12.4354
104.9094-0.3727-3.22085.88192.30817.1351-0.83050.0068-0.7432-0.56920.13640.92191.2077-0.29950.41570.947-0.2033-0.08260.41760.05870.664843.1236-16.7022-17.7586
112.2949-1.6651.32116.1244-0.04764.236-0.0260.5111-1.1167-0.82770.42940.24010.9499-0.24490.07430.6443-0.2640.030.4704-0.02120.390930.70031.664-11.9217
128.5258-3.9466-0.46839.41270.47359.47420.0474-0.88880.08931.05980.23760.13080.79220.2228-0.21610.71970.1215-0.06360.47170.05350.364336.19386.3478-0.1548
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 76:105)A76 - 105
2X-RAY DIFFRACTION2(chain A and resid 111:189)A111 - 189
3X-RAY DIFFRACTION3(chain A and resid 190:263)A190 - 263
4X-RAY DIFFRACTION4(chain A and resid 264:379)A264 - 379
5X-RAY DIFFRACTION5(chain A and resid 380:409)A380 - 409
6X-RAY DIFFRACTION6(chain A and resid 410:418)A410 - 418
7X-RAY DIFFRACTION7(chain A and resid 419:451)A419 - 451
8X-RAY DIFFRACTION8(chain A and resid 452:467)A452 - 467
9X-RAY DIFFRACTION9(chain A and resid 468:482)A468 - 482
10X-RAY DIFFRACTION10(chain A and resid 483:496)A483 - 496
11X-RAY DIFFRACTION11(chain B and resid 3:8)B3 - 8
12X-RAY DIFFRACTION12(chain B and resid 9:14)B9 - 14

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