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- PDB-8sg7: Adeno-Associated Virus Bat origin capsid protein basic regions in... -

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Basic information

Entry
Database: PDB / ID: 8sg7
TitleAdeno-Associated Virus Bat origin capsid protein basic regions in complex with importin-alpha 2
Components
  • Importin subunit alpha-1
  • VP1 capsid
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 / T=1 icosahedral viral capsid / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / cytoplasmic stress granule ...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 / T=1 icosahedral viral capsid / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / structural molecule activity / nucleoplasm / nucleus / 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 / Parvovirus coat protein VP2 ...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 / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
VP1 capsid / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Bat adeno-associated virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHoad, M. / Forwood, J.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Gen.Virol. / Year: 2024
Title: Structural basis for nuclear import of bat adeno-associated virus capsid protein.
Authors: Hoad, M. / Roby, J.A. / Forwood, J.K.
History
DepositionApr 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
Revision 1.2Jan 10, 2024Group: Data collection / Experimental preparation / Category: diffrn / exptl_crystal_grow
Item: _diffrn.ambient_temp / _exptl_crystal_grow.pdbx_details
Revision 1.3Mar 20, 2024Group: 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.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Importin subunit alpha-1
C: VP1 capsid


Theoretical massNumber of molelcules
Total (without water)61,5242
Polymers61,5242
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-1 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.065, 90.556, 99.816
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 VP1 capsid


Mass: 6255.124 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bat adeno-associated virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2Z4K4X6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 57.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.75M Na Citrate, 0.01M DTT, 0.1M HEPES, pH7.5

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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: Feb 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→19.96 Å / Num. obs: 32506 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 44.6 Å2 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.051 / Net I/σ(I): 8.8
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 1.335 / Mean I/σ(I) obs: 2 / Num. unique obs: 3158 / Rpim(I) all: 0.614

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.95 Å / SU ML: 0.243 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.3597
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.223 1440 5.04 %
Rwork0.184 27158 -
obs0.186 28598 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.68 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 0 41 3390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713418
X-RAY DIFFRACTIONf_angle_d0.93514665
X-RAY DIFFRACTIONf_chiral_restr0.0446568
X-RAY DIFFRACTIONf_plane_restr0.0062599
X-RAY DIFFRACTIONf_dihedral_angle_d16.64331231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.490.30081530.26252651X-RAY DIFFRACTION100
2.49-2.580.33061510.25292651X-RAY DIFFRACTION100
2.58-2.70.27811530.24762678X-RAY DIFFRACTION100
2.7-2.840.27011430.21962697X-RAY DIFFRACTION100
2.84-3.020.25121330.21692694X-RAY DIFFRACTION100
3.02-3.250.25131510.21462703X-RAY DIFFRACTION100
3.25-3.580.24531150.19382725X-RAY DIFFRACTION100
3.58-4.090.19861280.17032744X-RAY DIFFRACTION99.86
4.09-5.140.17451410.14262754X-RAY DIFFRACTION100
5.14-19.950.19491720.15742861X-RAY DIFFRACTION99.84

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