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- PDB-3ra2: Structural studies of AAV8 capsid transitions associated with end... -

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Basic information

Entry
Database: PDB / ID: 3ra2
TitleStructural studies of AAV8 capsid transitions associated with endosomal trafficking
ComponentsCapsid proteinCapsid
KeywordsVIRUS / beta barrel / Viral Capsid
Function / homology
Function and homology information


T=1 icosahedral viral capsid / structural molecule activity
Similarity search - Function
Empty Capsid Viral Protein 2 / Parvovirus coat protein VP1/VP2 / 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 / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Biological speciesAdeno-associated virus - 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNam, H.-J. / Gurda, B. / McKenna, R. / Porter, M. / Byrne, B. / Salganik, M. / Muzyczka, N. / Agbandje-McKenna, M.
CitationJournal: J.Virol. / Year: 2011
Title: Structural studies of adeno-associated virus serotype 8 capsid transitions associated with endosomal trafficking.
Authors: Nam, H.J. / Gurda, B.L. / McKenna, R. / Potter, M. / Byrne, B. / Salganik, M. / Muzyczka, N. / Agbandje-McKenna, M.
History
DepositionMar 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Other
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein


Theoretical massNumber of molelcules
Total (without water)58,5281
Polymers58,5281
Non-polymers00
Water1,56787
1
A: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)3,511,70260
Polymers3,511,70260
Non-polymers00
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein
x 5


  • icosahedral pentamer
  • 293 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)292,6425
Polymers292,6425
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
x 6


  • icosahedral 23 hexamer
  • 351 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)351,1706
Polymers351,1706
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: Capsid protein
x 10


  • crystal asymmetric unit, crystal frame
  • 585 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)585,28410
Polymers585,28410
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation9
Unit cell
Length a, b, c (Å)257.940, 257.940, 448.690
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.56302, 0.75475, 0.33668), (-0.75608, 0.30591, 0.57859), (0.33369, -0.58032, 0.74288)74.9098, -18.8907, -57.6322
3generate(-0.14074, 0.46213, 0.87557), (-0.46858, -0.81014, 0.35228), (0.87214, -0.36069, 0.33057)83.4409, -114.0371, -64.6731
4generate(-0.14511, -0.47022, 0.87054), (0.46672, -0.80834, -0.35883), (0.87242, 0.35422, 0.33676)15.213, -154.60001, -11.786
5generate(0.56178, -0.75844, 0.3304), (0.75688, 0.30997, -0.57537), (0.33397, 0.57331, 0.74819)-36.93, -84.216, 27.753
6generate(0.64274, 0.75508, 0.12937), (0.17955, -0.31265, 0.93275), (0.74475, -0.57628, -0.33652)87.985, -225.60001, 10.975
7generate(-0.16736, 0.64172, 0.74846), (0.64374, -0.50386, 0.57595), (0.74672, 0.57821, -0.32877)114.4044, -259.40659, 95.9389
8generate(-0.33335, -0.36312, 0.87007), (0.93412, -0.00223, 0.35696), (-0.12768, 0.93174, 0.33994)47.0159, -234.80569, 159.9783
9generate(0.37066, -0.86833, 0.32957), (0.64561, 0.49599, 0.58068), (-0.66768, -0.00246, 0.74444)-20.619, -185.83, 114.31
10generate(0.97584, -0.17742, -0.12755), (0.17754, 0.30347, 0.93616), (-0.12738, -0.93618, 0.32763)4.3195, -179.77, 21.995

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Components

#1: Protein Capsid protein / Capsid


Mass: 58528.367 Da / Num. of mol.: 1 / Fragment: UNP residues 220-738
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus - 8 / Strain: Serotype 8 / Cell line (production host): MAMMALIAN KIDNEY CELLS HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q8JQF8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE VIRUS CAPSID IS FROM AAV8 VIRUS BUT THE GENE ENCAPSULATED BY THE VIRUS WAS GFP. THE GENE CODING ...THE VIRUS CAPSID IS FROM AAV8 VIRUS BUT THE GENE ENCAPSULATED BY THE VIRUS WAS GFP. THE GENE CODING FOR GFP WAS NOT OBSERVED IN THE ELECTRON DENSITY MAP IN THIS STRUCTURE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 20 mM Tris pH 7.5, 4% PEG 8000, 1 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 238726 / Num. obs: 207183 / % possible obs: 86.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Rsym value: 0.114
Reflection shellResolution: 2.7→2.8 Å / % possible all: 58.2

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→40 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 10174 4.3 %RANDOM
Rwork0.2438 ---
obs0.244 197009 86.8 %-
all-238726 --
Solvent computationBsol: 23.4909 Å2
Displacement parametersBiso max: 97.62 Å2 / Biso mean: 36.4842 Å2 / Biso min: 5.62 Å2
Baniso -1Baniso -2Baniso -3
1-8.187 Å2-0 Å20 Å2
2--8.187 Å20 Å2
3----16.375 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4136 0 0 87 4223
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_scbond_it1.7742
X-RAY DIFFRACTIONc_mcangle_it2.0072
X-RAY DIFFRACTIONc_scangle_it2.8032.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param

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