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- PDB-2g8g: Structurally mapping the diverse phenotype of Adeno-Associated Vi... -

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Basic information

Entry
Database: PDB / ID: 2g8g
TitleStructurally mapping the diverse phenotype of Adeno-Associated Virus serotype 4
ComponentsCapsid
KeywordsVIRUS / Adeno-Associated Virus serotype 4 / Gene Therapy / 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
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / Capsid
Similarity search - Component
Biological speciesAdeno-associated virus - 4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsGovindasamy, L. / Padron, E. / McKenna, R. / Muzyczka, N. / Chiorini, J.A. / Agbandje-McKenna, M.
CitationJournal: J.Virol. / Year: 2006
Title: Structurally mapping the diverse phenotype of adeno-associated virus serotype 4.
Authors: Govindasamy, L. / Padron, E. / McKenna, R. / Muzyczka, N. / Kaludov, N. / Chiorini, J.A. / Agbandje-McKenna, M.
History
DepositionMar 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7742
Polymers58,4431
Non-polymers3311
Water27015
1
A: Capsid
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)3,526,428120
Polymers3,506,55560
Non-polymers19,87360
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
hetero molecules
x 5


  • icosahedral pentamer
  • 294 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)293,86910
Polymers292,2135
Non-polymers1,6565
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 353 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)352,64312
Polymers350,6556
Non-polymers1,9876
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
hetero molecules
x 15


  • crystal asymmetric unit, crystal frame
  • 882 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)881,60730
Polymers876,63915
Non-polymers4,96815
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation14
Unit cell
Length a, b, c (Å)339.6, 319.2, 285.0
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.5, -0.80901699, 0.30901699), (0.80901699, 0.30901699, -0.5), (0.30901699, 0.5, 0.80901699)
3generate(-0.30901699, -0.5, 0.80901699), (0.5, -0.80901699, -0.30901699), (0.80901699, 0.30901699, 0.5)
4generate(-0.30901699, 0.5, 0.80901699), (-0.5, -0.80901699, 0.30901699), (0.80901699, -0.30901699, 0.5)
5generate(0.5, 0.80901699, 0.30901699), (-0.80901699, 0.30901699, 0.5), (0.30901699, -0.5, 0.80901699)
6generate(-1), (-1), (1)
7generate(-0.80901699, -0.30901699, 0.5), (-0.30901699, -0.5, -0.80901699), (0.5, -0.80901699, 0.30901699)
8generate(-0.5, 0.80901699, 0.30901699), (-0.80901699, -0.30901699, -0.5), (-0.30901699, -0.5, 0.80901699)
9generate(0.5, 0.80901699, -0.30901699), (-0.80901699, 0.30901699, -0.5), (-0.30901699, 0.5, 0.80901699)
10generate(0.80901699, -0.30901699, -0.5), (-0.30901699, 0.5, -0.80901699), (0.5, 0.80901699, 0.30901699)
11generate(1), (-1), (-1)
12generate(0.30901699, 0.5, 0.80901699), (-0.5, 0.80901699, -0.30901699), (-0.80901699, -0.30901699, 0.5)
13generate(0.80901699, 0.30901699, 0.5), (0.30901699, 0.5, -0.80901699), (-0.5, 0.80901699, 0.30901699)
14generate(0.80901699, -0.30901699, 0.5), (0.30901699, -0.5, -0.80901699), (0.5, 0.80901699, -0.30901699)
15generate(0.30901699, -0.5, 0.80901699), (-0.5, -0.80901699, -0.30901699), (0.80901699, -0.30901699, -0.5)

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Components

#1: Protein Capsid /


Mass: 58442.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus - 4 / Genus: Dependovirus / Production host: Escherichia coli (E. coli) / References: UniProt: O41855
#2: Chemical ChemComp-D5M / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / Deoxyadenosine monophosphate


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


Mass: 18.015 Da / Num. of mol.: 15 / 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: 6

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: virus concentrations ranging from 2 to 4 mg/ml in 20 mM Tris HCl, pH 7.5, with 2 mM MgCl, 150 mM NaCl and 1 1.5% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.916 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 163565 / % possible obs: 75.9 % / Rsym value: 0.159 / Net I/σ(I): 4.41

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Processing

Software
NameVersionClassification
GLRFphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FPV

1fpv


Resolution: 3.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.273 -RANDOM
Rwork0.263 --
obs-163565 -
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4129 0 22 15 4166
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.601

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