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- PDB-2qa0: Structure of Adeno-Associated virus serotype 8 -

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Basic information

Entry
Database: PDB / ID: 2qa0
TitleStructure of Adeno-Associated virus serotype 8
ComponentsCapsid proteinCapsid
KeywordsVIRUS / beta-barrel / 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
Biological speciesAdeno-associated virus - 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNam, H.-J.
CitationJournal: J.Virol. / Year: 2007
Title: Structure of adeno-associated virus serotype 8, a gene therapy vector.
Authors: Nam, H.J. / Lane, M.D. / Padron, E. / Gurda, B. / McKenna, R. / Kohlbrenner, E. / Aslanidi, G. / Byrne, B. / Muzyczka, N. / Zolotukhin, S. / Agbandje-McKenna, M.
History
DepositionJun 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 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_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5512
Polymers58,5281
Non-polymers231
Water1,60389
1
A: Capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)3,513,081120
Polymers3,511,70260
Non-polymers1,37960
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
hetero molecules
x 5


  • icosahedral pentamer
  • 293 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)292,75710
Polymers292,6425
Non-polymers1155
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 351 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)351,30812
Polymers351,1706
Non-polymers1386
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
hetero molecules
x 10


  • crystal asymmetric unit, crystal frame
  • 586 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)585,51420
Polymers585,28410
Non-polymers23010
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation9
Unit cell
Length a, b, c (Å)254.840, 254.840, 445.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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(0.56366032, 0.7557619, 0.33333315), (-0.75576191, 0.30901699, 0.57734949), (0.33333314, -0.57734949, 0.74535668)74.07677, -18.82507, -56.58949
3generate(-0.14235213, 0.46708654, 0.87267751), (-0.46708655, -0.809017, 0.35682161), (0.8726775, -0.35682161, 0.33333513)82.74048, -113.29864, -63.20797
4generate(-0.14235213, -0.46708655, 0.87267751), (0.46708655, -0.80901699, -0.35682161), (0.87267751, 0.3568216, 0.33333513)14.01818, -152.86146, -10.70891
5generate(0.56366031, -0.75576191, 0.33333315), (0.75576191, 0.309017, -0.5773495), (0.33333315, 0.57734948, 0.74535668)-37.11825, -82.83905, 28.35576
6generate(0.64234943, 0.7557619, 0.12732301), (0.17841008, -0.309017, 0.93417254), (0.745357, -0.57734949, -0.33333243)86.99097, -223.05776, 11.03054
7generate(-0.1666682, 0.64549663, 0.74535616), (0.64549663, -0.50000001, 0.57735093), (0.74535617, 0.57735093, -0.3333318)113.14173, -256.8888, 95.97594
8generate(-0.3333341, -0.35682305, 0.87267731), (0.93417199, 0.35682305), (-0.12732269, 0.93417199, 0.3333341)46.46464, -232.33196, 159.18392
9generate(0.37267834, -0.8660254, 0.33333295), (0.64549663, 0.5, 0.57735093), (-0.66666705, -8.9E-7, 0.74535565)-20.89482, -183.32396, 113.30321
10generate(0.97568392, -0.17841009, -0.12732134), (0.17841008, 0.30901699, 0.93417255), (-0.12732134, -0.93417254, 0.33333307)4.15183, -177.59218, 21.73939

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Components

#1: Protein Capsid protein / Capsid


Mass: 58528.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus - 8 / Genus: Dependovirus / Strain: serotype 8 / Gene: VP1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: Q8JQF8
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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

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

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS F110.9175
SYNCHROTRONAPS 22-ID20.9764
Detector
TypeIDDetector
ADSC QUANTUM 41CCD
MARMOSAIC 300 mm CCD2CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91751
20.97641
ReflectionResolution: 2.6→40 Å / Num. all: 258784 / Num. obs: 202494 / % possible obs: 78.2 % / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Biso Wilson estimate: 47.6 Å2 / Rsym value: 0.11 / Net I/σ(I): 11.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 15888 / Rsym value: 0.338 / % possible all: 62.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LP3

1lp3


Resolution: 2.6→40 Å / Cross valid method: throughtout / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.259 9940 -random
Rwork0.255 ---
all-258784 --
obs-202050 78.1 %-
Displacement parametersBiso mean: 34.4 Å2
Baniso -1Baniso -2Baniso -3
1-7.91 Å20 Å20 Å2
2--7.91 Å20 Å2
3----15.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4136 0 1 89 4226
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg0.007
X-RAY DIFFRACTIONx_bond_d1.54
X-RAY DIFFRACTIONx_dihedral_angle_d26
X-RAY DIFFRACTIONx_improper_angle_d1.15

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