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- PDB-7l04: Crystal Structure of Adeno-Associated Virus Porcine Origin capsid... -

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Basic information

Entry
Database: PDB / ID: 7l04
TitleCrystal Structure of Adeno-Associated Virus Porcine Origin capsid protein in complex with Importin-alpha 2
Components
  • Importin subunit alpha-1
  • VP1
KeywordsTRANSPORT PROTEIN / Complex / transport / Nuclear Localization
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 / Importin subunit alpha-1
Similarity search - Component
Biological speciesAdeno-associated virus - Po1
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsHoad, M. / Forwood, J.
CitationJournal: To Be Published
Title: Crystal Structure of Adeno-Associated Virus Porcine Origin capsid protein in complex with Importin-alpha 2
Authors: Hoad, M. / Forwood, J.
History
DepositionDec 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 2.0Oct 13, 2021Group: Atomic model / Database references / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / pdbx_poly_seq_scheme / struct_ref / struct_ref_seq
Item: _atom_site.auth_seq_id / _database_2.pdbx_DOI ..._atom_site.auth_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_poly_seq_scheme.pdb_seq_num / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession
Revision 2.1Sep 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
Revision 2.2Oct 18, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.3Jan 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
C: VP1
E: Importin subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)56,5342
Polymers56,5342
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-0 kcal/mol
Surface area18660 Å2
Unit cell
Length a, b, c (Å)79.424, 89.350, 99.685
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/peptide VP1


Mass: 1265.566 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
#2: 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 (E. coli) / References: UniProt: P52293
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.13 Å3/Da / Density % sol: 60.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.6M 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: Oct 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.26→44.67 Å / Num. obs: 33929 / % possible obs: 99.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 34.4 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.124 / Net I/σ(I): 10.1
Reflection shellResolution: 2.26→2.33 Å / Rmerge(I) obs: 0.888 / Num. unique obs: 3034 / CC1/2: 0.759

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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: 6bw0

6bw0


Resolution: 2.26→44.67 Å / SU ML: 0.278 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.3607
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2338 1696 5.01 %
Rwork0.2147 32173 -
obs0.2157 33869 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.61 Å2
Refinement stepCycle: LAST / Resolution: 2.26→44.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3332 0 0 54 3386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00193400
X-RAY DIFFRACTIONf_angle_d0.49084628
X-RAY DIFFRACTIONf_chiral_restr0.0362556
X-RAY DIFFRACTIONf_plane_restr0.0032591
X-RAY DIFFRACTIONf_dihedral_angle_d12.75171254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.330.32171480.26852591X-RAY DIFFRACTION98.24
2.33-2.40.29311410.26742638X-RAY DIFFRACTION99.96
2.4-2.490.27731570.25852618X-RAY DIFFRACTION99.93
2.49-2.590.23851240.24922656X-RAY DIFFRACTION100
2.59-2.70.31761260.25272686X-RAY DIFFRACTION100
2.7-2.850.27621470.24842673X-RAY DIFFRACTION100
2.85-3.020.2481340.2522637X-RAY DIFFRACTION100
3.02-3.260.25751330.25092693X-RAY DIFFRACTION100
3.26-3.590.23271530.23082687X-RAY DIFFRACTION100
3.59-4.10.21221430.192696X-RAY DIFFRACTION100
4.1-5.170.18541420.16382736X-RAY DIFFRACTION100
5.17-44.670.2011480.17782862X-RAY DIFFRACTION99.8

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