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- PDB-4uaf: Importin alpha 1 delta IBB in complex with Influenza PB2 nuclear ... -

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Basic information

Entry
Database: PDB / ID: 4uaf
TitleImportin alpha 1 delta IBB in complex with Influenza PB2 nuclear localization domain
Components
  • Importin subunit alpha-1
  • Polymerase basic protein 2
KeywordsPROTEIN BINDING / importin karyopherin complex 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 / 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 ...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 / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding / postsynaptic density / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / glutamatergic synapse / host cell nucleus / RNA binding / nucleoplasm / 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
PHOSPHATE ION / Polymerase basic protein 2 / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.698 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

Downloads & links

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Assembly

Deposited unit
B: Importin subunit alpha-1
E: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9914
Polymers59,8012
Non-polymers1902
Water8,467470
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-10 kcal/mol
Surface area21370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.131, 90.188, 100.772
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: 50461.285 Da / Num. of mol.: 1
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-AI / References: UniProt: P52293
#2: Protein Polymerase basic protein 2 / RNA-directed RNA polymerase subunit P3


Mass: 9339.651 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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.93 Å3/Da / Density % sol: 58.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.49 M Na phosphate monobasic 0.91 M K phosphate dibasic pH 6.9
PH range: 6.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.7→15 Å / Num. obs: 76101 / % possible obs: 97.5 % / Redundancy: 4.5 % / Net I/σ(I): 48.5

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementResolution: 1.698→14.963 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1927 3722 2.62 %random selection
Rwork0.1646 ---
obs0.1654 141898 94.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.698→14.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3791 0 10 470 4271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073880
X-RAY DIFFRACTIONf_angle_d1.065279
X-RAY DIFFRACTIONf_dihedral_angle_d11.8721440
X-RAY DIFFRACTIONf_chiral_restr0.043636
X-RAY DIFFRACTIONf_plane_restr0.006674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6977-1.71920.27051300.26744883X-RAY DIFFRACTION90
1.7192-1.74180.29871400.26565067X-RAY DIFFRACTION94
1.7418-1.76560.261370.25415126X-RAY DIFFRACTION94
1.7656-1.79080.25821360.24585049X-RAY DIFFRACTION94
1.7908-1.81740.24341370.24085075X-RAY DIFFRACTION94
1.8174-1.84580.26091420.23695144X-RAY DIFFRACTION94
1.8458-1.8760.27391390.22515122X-RAY DIFFRACTION94
1.876-1.90830.27241350.2145058X-RAY DIFFRACTION95
1.9083-1.94290.21921400.20155152X-RAY DIFFRACTION95
1.9429-1.98020.22651350.1825185X-RAY DIFFRACTION95
1.9802-2.02050.22981320.17725169X-RAY DIFFRACTION96
2.0205-2.06440.19361410.16325132X-RAY DIFFRACTION96
2.0644-2.11220.17251400.15775239X-RAY DIFFRACTION97
2.1122-2.16490.16951470.15435234X-RAY DIFFRACTION97
2.1649-2.22330.18391360.1495237X-RAY DIFFRACTION97
2.2233-2.28850.15781420.14385209X-RAY DIFFRACTION97
2.2885-2.36210.16621410.14645245X-RAY DIFFRACTION97
2.3621-2.44610.20341450.15085270X-RAY DIFFRACTION98
2.4461-2.54360.18151460.1485274X-RAY DIFFRACTION98
2.5436-2.65880.18831450.15925351X-RAY DIFFRACTION98
2.6588-2.79810.18491430.14975243X-RAY DIFFRACTION98
2.7981-2.97210.19481430.16055303X-RAY DIFFRACTION98
2.9721-3.19950.17651390.165266X-RAY DIFFRACTION97
3.1995-3.51770.20761400.15695208X-RAY DIFFRACTION97
3.5177-4.01810.16551370.13985056X-RAY DIFFRACTION94
4.0181-5.03020.18911210.1434772X-RAY DIFFRACTION88
5.0302-14.96360.17011130.19524107X-RAY DIFFRACTION76
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)
10.8092-0.36120.052.42820.45840.58630.03920.0097-0.01210.05060.02470.03120.0628-0.0588-0.07520.1314-0.0135-0.00760.157-0.00580.12384.45745.9144-15.7731
21.9573-0.2631-0.93951.49090.5581.70110.01-0.4440.1790.16460.0544-0.1191-0.00290.235-0.01060.17680.00380.00340.2725-0.07450.2647-6.122436.513413.8173
36.14730.50180.92032.1335-0.43746.9576-0.4586-0.86550.68570.08680.0602-0.2834-0.16780.02270.39370.24750.01480.00440.4188-0.1420.572513.596538.425519.3614
45.16485.23364.80075.31094.8644.4442-0.07460.5336-0.23230.1110.0486-0.71890.09090.11290.14830.5669-0.12710.02880.6543-0.02960.733114.541139.267210.1662
54.54030.3968-0.8673.4828-5.36078.2807-0.0309-0.92220.56190.4826-0.0501-0.439-0.74250.2440.0640.29140.064-0.03260.5164-0.23890.556814.457440.108220.5176
65.22694.78033.52674.40693.44614.4768-0.06820.179-1.50390.3799-0.1469-0.6091.52850.0980.05630.66450.04990.19690.4396-0.17280.70670.79325.85567.6167
75.2808-1.54070.62666.133-0.69232.280.1838-0.70450.75370.746-0.24270.9472-0.2102-0.68590.1840.2376-0.02540.08160.3072-0.04230.2763-2.93936.0423-8.341
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 72 through 278 )
2X-RAY DIFFRACTION2chain 'B' and (resid 279 through 496 )
3X-RAY DIFFRACTION3chain 'E' and (resid 687 through 709 )
4X-RAY DIFFRACTION4chain 'E' and (resid 710 through 720 )
5X-RAY DIFFRACTION5chain 'E' and (resid 721 through 736 )
6X-RAY DIFFRACTION6chain 'E' and (resid 737 through 747 )
7X-RAY DIFFRACTION7chain 'E' and (resid 748 through 758 )

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