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- PDB-8fk3: Adeno-Associated Virus Porcine Origin capsid protein basic region... -

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Basic information

Entry
Database: PDB / ID: 8fk3
TitleAdeno-Associated Virus Porcine Origin capsid protein basic regions in complex with Importin-alpha 2
Components
  • Importin subunit alpha-1
  • VP1
KeywordsTRANSPORT PROTEIN / importin / alpha / adeno associated / complex / basic regions / transport / nucleus
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 / T=1 icosahedral viral capsid / cytoplasmic stress granule / protein import into nucleus / host cell ...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 / T=1 icosahedral viral capsid / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / structural molecule activity / nucleoplasm / cytosol
Similarity search - Function
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. / Phospholipase A2-like domain / Phospholipase A2-like domain / Armadillo/plakoglobin ARM repeat profile. ...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. / Phospholipase A2-like domain / Phospholipase A2-like domain / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP1/VP2 / Capsid/spike protein, ssDNA virus / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
VP1 / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Adeno-associated virus - Po1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHoad, M. / Forwood, J.K. / Roby, J.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Viruses / Year: 2023
Title: Structural Characterization of Porcine Adeno-Associated Virus Capsid Protein with Nuclear Trafficking Protein Importin Alpha Reveals a Bipartite Nuclear Localization Signal.
Authors: Hoad, M. / Cross, E.M. / Donnelly, C.M. / Sarker, S. / Roby, J.A. / Forwood, J.K.
History
DepositionDec 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 31, 2023Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
Revision 1.4Jan 10, 2024Group: Data collection / Experimental preparation / Category: diffrn / exptl_crystal_grow
Item: _diffrn.ambient_temp / _exptl_crystal_grow.pdbx_details

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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: VP1


Theoretical massNumber of molelcules
Total (without water)59,9142
Polymers59,9142
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-3 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.149, 89.457, 99.394
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: 55268.473 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 BL21(DE3) (bacteria) / References: UniProt: P52293
#2: Protein/peptide VP1


Mass: 4645.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus - Po1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C0LA97
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.75M Na Citrate, 0.01M DTT, 0.1M HEPES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→19.96 Å / Num. obs: 21468 / % possible obs: 97.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 50.75 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.6
Reflection shellResolution: 2.6→2.72 Å / Rmerge(I) obs: 0.643 / Num. unique obs: 2616 / CC1/2: 0.639

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Processing

Software
NameVersionClassification
REFMAC1.18.2_3874refinement
PHENIX1.18.2_3874refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4oih

4oih


Resolution: 2.6→19.96 Å / SU ML: 0.339 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.3277
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2495 1031 4.81 %
Rwork0.2119 20405 -
obs0.2139 21436 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.71 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3279 0 0 25 3304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00343337
X-RAY DIFFRACTIONf_angle_d0.57224551
X-RAY DIFFRACTIONf_chiral_restr0.0359557
X-RAY DIFFRACTIONf_plane_restr0.0031578
X-RAY DIFFRACTIONf_dihedral_angle_d3.3868457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.740.32661360.28312910X-RAY DIFFRACTION98.8
2.74-2.910.30061440.25192914X-RAY DIFFRACTION98.52
2.91-3.130.31621450.2522896X-RAY DIFFRACTION98.48
3.13-3.450.26061590.23452870X-RAY DIFFRACTION96.93
3.45-3.940.26551520.20632893X-RAY DIFFRACTION97.38
3.94-4.950.21871280.18222958X-RAY DIFFRACTION97.35
4.95-19.960.21371670.19542964X-RAY DIFFRACTION95.11

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