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- PDB-9cft: Adeno-associated virus serotype 6 basic regions in complex with i... -

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Basic information

Entry
Database: PDB / ID: 9cft
TitleAdeno-associated virus serotype 6 basic regions in complex with importin alpha 2
Components
  • Capsid protein VP1
  • Importin subunit alpha-1
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 / protein import into nucleus / cytoplasmic stress granule / 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 / protein import into nucleus / cytoplasmic stress granule / 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 VP2 / Capsid/spike protein, ssDNA virus / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Capsid protein VP1 / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Adeno-associated virus - 6
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHoad, M. / Forwood, J.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Virol. / Year: 2025
Title: Structural basis for nuclear import of adeno-associated virus serotype 6 capsid protein.
Authors: Hoad, M. / Nematollahzadeh, S. / Petersen, G.F. / Roby, J.A. / Alvisi, G. / Forwood, J.K.
History
DepositionJun 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 12, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year

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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: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7923
Polymers61,7002
Non-polymers921
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.013, 89.319, 101.644
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 / Fragment: UNP residues 70-529
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 Capsid protein VP1


Mass: 6431.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus - 6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O56137
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.65 M Na citrate, 0.01 M DTT, 0.1 M HEPES, pH 7.0

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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 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→19.82 Å / Num. obs: 32611 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 43.04 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.5
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 316 / CC1/2: 0.57

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Processing

Software
NameVersionClassification
PHENIX1.211.5286refinement
XDS1.18.2_3874data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.82 Å / SU ML: 0.2194 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5497
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2379 1620 4.98 %
Rwork0.2144 30920 -
obs0.2155 32540 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.75 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3378 0 6 32 3416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00233441
X-RAY DIFFRACTIONf_angle_d0.48854678
X-RAY DIFFRACTIONf_chiral_restr0.0353562
X-RAY DIFFRACTIONf_plane_restr0.0042597
X-RAY DIFFRACTIONf_dihedral_angle_d13.12941266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.30031500.30082524X-RAY DIFFRACTION99.59
2.37-2.440.28051360.28892507X-RAY DIFFRACTION99.7
2.44-2.530.28841330.27562553X-RAY DIFFRACTION99.93
2.53-2.630.28931340.26132546X-RAY DIFFRACTION100
2.63-2.750.3041270.27412563X-RAY DIFFRACTION99.96
2.75-2.90.27771260.24192545X-RAY DIFFRACTION99.96
2.9-3.080.28121410.26052561X-RAY DIFFRACTION100
3.08-3.310.25451350.24972575X-RAY DIFFRACTION99.93
3.31-3.650.21221180.22672583X-RAY DIFFRACTION99.85
3.65-4.170.22071490.19362580X-RAY DIFFRACTION100
4.17-5.240.22081210.17362655X-RAY DIFFRACTION100
5.24-19.820.19971500.16892728X-RAY DIFFRACTION99.97

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