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Basic information

Entry
Database: PDB / ID: 3oah
TitleStructural Characterization of the Dual Glycan Binding Adeno-Associated Virus Serotype 6
ComponentsCapsid protein VP1
KeywordsVIRUS / Beta-barrel / ssDNA binding / ssDNA / icosahedral virus
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
6-AMINOPYRIMIDIN-2(1H)-ONE / Chem-OAH / Capsid protein VP1
Similarity search - Component
Biological speciesAdeno-associated virus - 6
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsNg, R. / Agbandje-McKenna, M.
CitationJournal: J.Virol. / Year: 2010
Title: Structural characterization of the dual glycan binding adeno-associated virus serotype 6.
Authors: Ng, R. / Govindasamy, L. / Gurda, B.L. / McKenna, R. / Kozyreva, O.G. / Samulski, R.J. / Parent, K.N. / Baker, T.S. / Agbandje-McKenna, M.
History
DepositionAug 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 19, 2011Group: Other
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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1063
Polymers59,6641
Non-polymers4422
Water19811
1
A: Capsid protein VP1
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)3,606,378180
Polymers3,579,83960
Non-polymers26,539120
Water1,08160
TypeNameSymmetry operationNumber
point symmetry operation11*11
point symmetry operation11*21
point symmetry operation11*31
point symmetry operation11*41
point symmetry operation11*51
point symmetry operation11*61
point symmetry operation11*71
point symmetry operation11*81
point symmetry operation11*91
point symmetry operation11*101
point symmetry operation12*11
point symmetry operation12*21
point symmetry operation12*31
point symmetry operation12*41
point symmetry operation12*51
point symmetry operation12*61
point symmetry operation12*71
point symmetry operation12*81
point symmetry operation12*91
point symmetry operation12*101
point symmetry operation13*11
point symmetry operation13*21
point symmetry operation13*31
point symmetry operation13*41
point symmetry operation13*51
point symmetry operation13*61
point symmetry operation13*71
point symmetry operation13*81
point symmetry operation13*91
point symmetry operation13*101
point symmetry operation14*11
point symmetry operation14*21
point symmetry operation14*31
point symmetry operation14*41
point symmetry operation14*51
point symmetry operation14*61
point symmetry operation14*71
point symmetry operation14*81
point symmetry operation14*91
point symmetry operation14*101
point symmetry operation15*11
point symmetry operation15*21
point symmetry operation15*31
point symmetry operation15*41
point symmetry operation15*51
point symmetry operation15*61
point symmetry operation15*71
point symmetry operation15*81
point symmetry operation15*91
point symmetry operation15*101
point symmetry operation16*11
point symmetry operation16*21
point symmetry operation16*31
point symmetry operation16*41
point symmetry operation16*51
point symmetry operation16*61
point symmetry operation16*71
point symmetry operation16*81
point symmetry operation16*91
point symmetry operation16*101
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation11*11
3
A: Capsid protein VP1
hetero molecules
x 5


  • icosahedral pentamer
  • 301 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)300,53215
Polymers298,3205
Non-polymers2,21210
Water905
TypeNameSymmetry operationNumber
point symmetry operation11*11
point symmetry operation11*21
point symmetry operation11*31
point symmetry operation11*41
point symmetry operation11*51
4
A: Capsid protein VP1
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 361 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)360,63818
Polymers357,9846
Non-polymers2,65412
Water1086
TypeNameSymmetry operationNumber
point symmetry operation11*11
point symmetry operation11*21
point symmetry operation11*61
point symmetry operation11*101
point symmetry operation13*31
point symmetry operation13*41
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame10*11
6
A: Capsid protein VP1
hetero molecules
x 10


  • crystal asymmetric unit, crystal frame
  • 601 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)601,06330
Polymers596,64010
Non-polymers4,42320
Water18010
TypeNameSymmetry operationNumber
transform to crystal frame10*21
point symmetry operation11*11
point symmetry operation11*21
point symmetry operation11*31
point symmetry operation11*41
point symmetry operation11*51
point symmetry operation11*61
point symmetry operation11*71
point symmetry operation11*81
point symmetry operation11*91
point symmetry operation11*101
Unit cell
Length a, b, c (Å)263.000, 263.000, 609.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.49994, 0.86606, -0.00096), (-0.64497, 0.37305, 0.66697), (0.57799, -0.33283, 0.74509)-131.21872, -172.5981, 152.95435
3generate(0.80776, 0.11041, -0.57908), (0.46813, 0.4769, 0.74392), (0.35831, -0.87199, 0.33353)83.76004, -49.62574, 248.36168
4generate(0.80892, 0.46906, 0.35444), (-0.1073, -0.47496, 0.87344), (0.57804, -0.74458, -0.33388)-132.55228, -79.47877, 402.95685
5generate(0.31093, -0.17614, 0.93397), (-0.17612, -0.97634, -0.12549), (0.93397, -0.12547, -0.3346)-266.70798, 152.013, 403.02133
6generate(0.30677, 0.75759, 0.57615), (0.7576, -0.56079, 0.33401), (0.57614, 0.33403, -0.74598)-265.44373, 150.20345, 404.55695
7generate(0.81032, -0.46586, -0.35547), (-0.11027, 0.47455, -0.87329), (0.57552, 0.74684, 0.33317)82.41815, 202.38565, 154.35345
8generate(0.80892, -0.10724, 0.57805), (0.46907, -0.47503, -0.74453), (0.35444, 0.87341, -0.33395)-134.23608, 324.4563, 250.96318
9generate(0.49992, -0.64495, 0.57803), (0.86607, 0.37301, -0.33285), (-0.00095, 0.66701, 0.74505)-134.14249, 228.95674, 1.03812
10generate(0.002, -0.9335, 0.35858), (0.35675, -0.33432, -0.87233), (0.9342, 0.12967, 0.33236)-133.29675, 324.92532, 248.47168
Detailsnon-envelope T=1 icosahedron, 10 monomer in the assymmetric unit cell of the crystal

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Components

#1: Protein Capsid protein VP1


Mass: 59663.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus - 6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O56137
#2: Chemical ChemComp-CYT / 6-AMINOPYRIMIDIN-2(1H)-ONE / CYTOSINE


Mass: 111.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5N3O
#3: Chemical ChemComp-OAH / 9-(2-deoxy-5-O-phosphono-alpha-D-threo-pentofuranosyl)-9H-purin-6-amine


Mass: 331.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 25mM Tris-HCl pH7.5 with 60 mM MgCl2 and 100mM NaCl, 4% PEG6000, and 25%glycerol, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.917 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 15, 2009 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 119617 / % possible obs: 72.3 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.15 / Rsym value: 0.154 / Net I/σ(I): 6.5
Reflection shellResolution: 3→3.11 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.607 / Mean I/σ(I) obs: 2.5 / Num. unique all: 8285 / Rsym value: 0.443 / % possible all: 50.5

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Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AAV1

Resolution: 3→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2875 5549 Random
Rwork0.2747 --
obs-119617 -
Refinement stepCycle: LAST / Resolution: 3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4117 0 30 11 4158
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.48
X-RAY DIFFRACTIONc_bond_d0.009

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