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- PDB-3ntt: Structural insights of Adeno-Associated virus 5. A gene therapy V... -

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Basic information

Entry
Database: PDB / ID: 3ntt
TitleStructural insights of Adeno-Associated virus 5. A gene therapy Vector for Cystic Fibrosis
ComponentsCapsid proteinCapsid
KeywordsVIRUS / Adeno-associated virus 5 / gene therapy vector / cystic fibrosis / sialic acid receptor / 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 - 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsGovindasamy, L. / DiMattia, M. / Chiorini, J.A. / McKenna, R. / Muzyczka, N. / Agbandje-McKenna, M.
CitationJournal: J.Virol. / Year: 2013
Title: Structural insights into adeno-associated virus serotype 5.
Authors: Govindasamy, L. / DiMattia, M.A. / Gurda, B.L. / Halder, S. / McKenna, R. / Chiorini, J.A. / Muzyczka, N. / Zolotukhin, S. / Agbandje-McKenna, M.
History
DepositionJul 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Other
Revision 1.2Aug 10, 2016Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 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 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6585
Polymers80,4971
Non-polymers1614
Water0
1
A: Capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)4,839,509300
Polymers4,829,84560
Non-polymers9,664240
Water0
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
  • 403 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)403,29225
Polymers402,4875
Non-polymers80520
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 484 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)483,95130
Polymers482,9846
Non-polymers96624
Water0
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 60


  • crystal asymmetric unit, crystal frame
  • 4.84 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)4,839,509300
Polymers4,829,84560
Non-polymers9,664240
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)264.7, 447.9, 629.7
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.581885, -0.756835, 0.297674), (0.270805, 0.525445, 0.806581), (-0.76686, -0.388726, 0.510703)64.23468, -131.69117, 211.13416
3generate(-0.094638, -0.95378, -0.285213), (-0.318664, -0.242401, 0.916349), (-0.943131, 0.177609, -0.280995)264.12958, -13.1959, 320.89386
4generate(-0.094638, -0.318664, -0.943131), (-0.95378, -0.242401, 0.177609), (-0.285213, 0.916349, -0.280995)323.43675, 191.72937, 177.59492
5generate(0.581885, 0.270805, -0.76686), (-0.756835, 0.525445, -0.388726), (0.297674, 0.806581, 0.510703)160.19569, 199.88488, -20.72839
6generate(-0.944303, -0.176862, -0.277508), (-0.176862, -0.438381, 0.881216), (-0.277508, 0.881216, 0.382685)244.12326, 4.83225, 45.91641
7generate(-0.384562, 0.729625, -0.565473), (-0.897398, -0.439041, 0.043803), (-0.216306, 0.524299, 0.823603)148.16597, 237.25732, -7.15972
8generate(0.407453, 0.894242, 0.185239), (-0.674668, 0.431463, -0.598884), (-0.615471, 0.119043, 0.779117)-92.01201, 246.67935, 83.79112
9generate(0.337204, 0.089493, 0.937168), (0.183523, 0.970125, -0.158674), (-0.92337, 0.225498, 0.310706)-144.49287, 20.07742, 193.07797
10generate(-0.498228, -0.572486, 0.651175), (0.491184, 0.432531, 0.756079), (-0.714498, 0.696546, 0.065697)63.25015, -129.39231, 169.67011
11generate(0.712332, -0.383283, 0.587944), (-0.383283, -0.914207, -0.131604), (0.587944, -0.131604, -0.798124)-49.98288, 284.72785, 331.18579
12generate(-0.14017, -0.969061, 0.203159), (-0.369677, -0.139126, -0.918685), (0.918527, -0.203875, -0.338738)170.38351, 352.71479, 217.77185
13generate(-0.499783, -0.482076, -0.719597), (0.451718, 0.563798, -0.691435), (0.739032, -0.670622, -0.064015)331.89027, 153.32448, 232.10252
14generate(0.130465, 0.404675, -0.905106), (0.945761, 0.223148, 0.236095), (0.297515, -0.886816, -0.353613)211.34054, -37.89244, 354.3733
15generate(0.879593, 0.465732, -0.097002), (0.429702, -0.690309, 0.58209), (0.204137, -0.553684, -0.807318)-24.67004, 43.31931, 415.61013
16generate(-0.768028, 0.560145, -0.310436), (0.560145, 0.352589, -0.749612), (-0.310436, -0.749612, -0.58456)149.05797, 180.69911, 437.43359
17generate(-0.057154, 0.996271, 0.06464), (0.996271, 0.052722, 0.068302), (0.06464, 0.068302, -0.995568)-39.5858, 11.97827, 392.7895
18generate(0.186968, 0.541615, 0.819571), (0.541615, -0.752861, 0.373971), (0.819571, 0.373971, -0.434107)-160.80949, 83.45127, 177.74829
19generate(-0.37303, -0.175504, 0.911069), (-0.175504, -0.950872, -0.25503), (0.911069, -0.25503, 0.323903)-47.08606, 296.34485, 89.4896
20generate(-0.963251, -0.164051, 0.212687), (-0.164051, -0.267667, -0.949443), (0.212687, -0.949443, 0.230917)144.42256, 356.44733, 249.98394
21generate(-0.217546, -0.615025, 0.757903), (-0.557025, 0.715864, 0.421024), (-0.801497, -0.330579, -0.498318)22.4354, -4.53798, 412.74092
22generate(-0.874345, -0.453132, -0.173761), (-0.453132, 0.63406, 0.626609), (-0.173761, 0.626609, -0.759716)249.47407, -45.6987, 299.5794
23generate(-0.498228, 0.491184, -0.714498), (-0.572486, 0.432531, 0.696546), (0.651175, 0.756079, 0.065697)216.29736, -26.0071, 45.49705
24generate(0.391023, 0.912911, -0.117026), (-0.750143, 0.389783, 0.534186), (0.533279, -0.121092, 0.837228)-31.24565, 27.32369, 1.62704
25generate(0.564494, 0.229236, 0.792968), (-0.740588, 0.564893, 0.363904), (-0.364522, -0.792684, 0.488648)-151.05893, 40.59233, 228.59624
26generate(0.10388, 0.975968, -0.191561), (0.282554, 0.155708, 0.94653), (0.95361, -0.152452, -0.259588)1.15552, -117.72956, 192.59854
27generate(0.471643, 0.508662, 0.720288), (-0.519275, -0.499971, 0.693096), (0.712675, -0.700922, 0.028328)-161.14315, 79.75952, 219.12197
28generate(-0.14017, -0.369677, 0.918527), (-0.969061, -0.139126, -0.203875), (0.203159, -0.918685, -0.338738)-45.75613, 258.58206, 363.18664
29generate(-0.886054, -0.445215, 0.129196), (-0.445215, 0.739568, -0.5048), (0.129196, -0.5048, -0.853513)187.85565, 171.61138, 425.70007
30generate(-0.735223, 0.38644, -0.556876), (0.328326, 0.921785, 0.206189), (0.593, -0.031242, -0.804596)216.84865, -60.962, 320.27083
31generate(0.526368, 0.545899, -0.651867), (-0.423626, -0.496358, -0.757739), (-0.737209, 0.674998, -0.03001)109.20109, 366.56751, 193.64119
32generate(0.954009, 0.141864, 0.264087), (0.200162, 0.354359, -0.913436), (-0.223165, 0.924286, 0.309666)-66.50931, 244.73734, 51.05944
33generate(0.391023, -0.750143, 0.533279), (0.912911, 0.389783, -0.121092), (-0.117026, 0.534186, 0.837228)31.84678, 18.0712, -19.61469
34generate(-0.384562, -0.897398, -0.216306), (0.729625, -0.439041, 0.524299), (-0.565473, 0.043803, 0.823603)268.3446, -0.186, 79.28804
35generate(-0.300914, -0.0964, -0.948767), (-0.0964, -0.986707, 0.13083), (-0.948767, 0.13083, 0.287621)316.15219, 215.19656, 211.08743
36generate(-0.412702, -0.906842, 0.085524), (0.698098, -0.375214, -0.609815), (0.585095, -0.191967, 0.787916)210.40634, 225.95924, 15.55513
37generate(-0.551307, -0.197394, -0.810614), (0.772246, -0.488449, -0.406269), (-0.315748, -0.849973, 0.421722)321.37675, 191.46104, 244.77497
38generate(0.247375, 0.628636, -0.737308), (0.628636, -0.683188, -0.371579), (-0.737308, -0.371579, -0.564187)140.81035, 219.61305, 425.46679
39generate(0.879593, 0.429702, 0.204137), (0.465732, -0.690309, -0.553684), (-0.097002, 0.58209, -0.807318)-81.75624, 271.51014, 307.92063
40generate(0.471643, -0.519275, 0.712675), (0.508662, -0.499971, -0.700922), (0.720288, 0.693096, 0.028328)-38.74355, 275.43231, 54.5813
41generate(-0.217546, -0.557025, -0.801497), (-0.615025, 0.715864, -0.330579), (0.757903, 0.421024, -0.498318)333.16342, 153.49032, 190.58296
42generate(0.337204, 0.183523, -0.92337), (0.089493, 0.970125, 0.225498), (0.937168, -0.158674, 0.310706)223.32134, -50.08511, 78.60951
43generate(0.954009, 0.200162, -0.223165), (0.141864, 0.354359, 0.924286), (0.264087, -0.913436, 0.309666)25.85809, -124.48319, 225.30472
44generate(0.780465, -0.530103, 0.331459), (-0.530287, -0.280465, 0.800084), (-0.331165, -0.800206, -0.5)13.66117, 33.1117, 427.94079
45generate(0.056404, -0.99807, -0.025969), (-0.99807, -0.057043, 0.024535), (-0.025969, 0.024535, -0.999362)203.58631, 204.90878, 406.48156
46generate(0.526368, -0.423626, -0.737209), (0.545899, -0.496358, 0.674998), (-0.651867, -0.757739, -0.03001)240.56177, -8.37137, 354.75835
47generate(0.756902, -0.334394, -0.561498), (-0.334394, -0.936354, 0.106871), (-0.561498, 0.106871, -0.820548)174.51071, 234.57544, 406.33738
48generate(0.780465, -0.530287, -0.331165), (-0.530103, -0.280465, -0.800206), (0.331459, 0.800084, -0.5)148.61545, 358.9694, 182.95011
49generate(0.564494, -0.740588, -0.364522), (0.229236, 0.564893, -0.792684), (0.792968, 0.363904, 0.488648)198.66236, 192.90229, -6.68984
50generate(0.407453, -0.674668, -0.615471), (0.894242, 0.431463, 0.119043), (0.185239, -0.598884, 0.779117)255.4883, -34.1268, 99.49349
51generate(-0.412702, 0.698098, 0.585095), (-0.906842, -0.375214, -0.191967), (0.085524, -0.609815, 0.787916)-80.00778, 278.57455, 107.54227
52generate(-0.499783, 0.451718, 0.739032), (-0.482076, 0.563798, -0.670622), (-0.719597, -0.691435, -0.064015)-74.91722, 229.20537, 359.69909
53generate(-0.735223, 0.328326, 0.593), (0.38644, 0.921785, -0.031242), (-0.556876, 0.206189, -0.804596)-10.47304, -17.59917, 391.01623
54generate(-0.793652, 0.498446, 0.348811), (0.498446, 0.204021, 0.842572), (0.348811, 0.842572, -0.41037)24.26509, -120.76357, 158.21446
55generate(-0.594322, 0.726977, 0.343926), (-0.300847, -0.597569, 0.743238), (0.745837, 0.338254, 0.573857)-18.70975, 62.28186, -16.98208
56generate(0.10388, 0.282554, 0.95361), (0.975968, 0.155708, -0.152452), (-0.191561, 0.94653, -0.259588)-150.51905, 46.5657, 161.65221
57generate(-0.594322, -0.300847, 0.745837), (0.726977, -0.597569, 0.338254), (0.343926, 0.743238, 0.573857)20.28352, 56.56351, -30.11019
58generate(-0.99925, 0.0018, -0.03867), (0.0018, -0.99568, -0.092838), (-0.03867, -0.092838, 0.99493)179.19785, 253.37216, 15.26473
59generate(-0.551307, 0.772246, -0.315748), (-0.197394, -0.488449, -0.849973), (-0.810614, -0.406269, 0.421722)106.60974, 365.00878, 235.07038
60generate(0.130465, 0.945761, 0.297515), (0.404675, 0.223148, -0.886816), (-0.905106, 0.236095, -0.353613)-97.16651, 237.19536, 325.54281
DetailsThe asymmetric unit contains 60 copies of capsid protein

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Components

#1: Protein Capsid protein / Capsid


Mass: 80497.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus - 5 / Gene: cap, VP1 / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9YIJ1
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

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Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20mM Tris HCL, 350mM NaCl, MgCl2, 1.5% PEK 8K, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.1
SYNCHROTRONCHESS F120.924
Detector
TypeIDDetector
ADSC QUANTUM 3151CCD
ADSC QUANTUM 42CCD
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.9241
ReflectionResolution: 3.45→50 Å / Num. all: 1718943 / Num. obs: 762314 / % possible obs: 78.6 % / Redundancy: 2.3 % / Biso Wilson estimate: 46.83 Å2 / Rsym value: 0.161 / Net I/σ(I): 7.9
Reflection shellResolution: 3.45→3.57 Å / Rsym value: 0.26 / % possible all: 58.5

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Processing

Software
NameVersionClassification
ADSC Quantumdata collection
PHENIXrefinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2g8g

2g8g


Resolution: 3.45→49.959 Å / SU ML: 0.36 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2515 761855 100 %
Rwork0.2515 --
obs0.2515 761855 78.56 %
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.07 Å2 / ksol: 0.395 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.997 Å2-0 Å20 Å2
2---7.3301 Å20 Å2
3---0.3331 Å2
Refinement stepCycle: LAST / Resolution: 3.45→49.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4111 0 9 0 4120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005254640
X-RAY DIFFRACTIONf_angle_d1.015347880
X-RAY DIFFRACTIONf_dihedral_angle_d19.56991320
X-RAY DIFFRACTIONf_chiral_restr0.0736120
X-RAY DIFFRACTIONf_plane_restr0.00746260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.48920.3334172360.333417236X-RAY DIFFRACTION54
3.4892-3.53020.3257189660.325718966X-RAY DIFFRACTION59
3.5302-3.57330.3257201900.325720190X-RAY DIFFRACTION63
3.5733-3.61850.3246207130.324620713X-RAY DIFFRACTION64
3.6185-3.66610.3098210180.309821018X-RAY DIFFRACTION65
3.6661-3.71630.3029213650.302921365X-RAY DIFFRACTION67
3.7163-3.76940.2928219610.292821961X-RAY DIFFRACTION68
3.7694-3.82560.2889224560.288922456X-RAY DIFFRACTION70
3.8256-3.88540.2881230840.288123084X-RAY DIFFRACTION72
3.8854-3.9490.2788233510.278823351X-RAY DIFFRACTION73
3.949-4.01710.279238860.27923886X-RAY DIFFRACTION74
4.0171-4.09010.2726246150.272624615X-RAY DIFFRACTION76
4.0901-4.16880.2685249250.268524925X-RAY DIFFRACTION77
4.1688-4.25380.264252300.26425230X-RAY DIFFRACTION78
4.2538-4.34630.2481256680.248125668X-RAY DIFFRACTION80
4.3463-4.44730.234257630.23425763X-RAY DIFFRACTION80
4.4473-4.55840.2343266220.234326622X-RAY DIFFRACTION82
4.5584-4.68160.2294269450.229426945X-RAY DIFFRACTION84
4.6816-4.81930.2232272290.223227229X-RAY DIFFRACTION84
4.8193-4.97470.2233273780.223327378X-RAY DIFFRACTION85
4.9747-5.15230.2144278010.214427801X-RAY DIFFRACTION86
5.1523-5.35840.2206282850.220628285X-RAY DIFFRACTION88
5.3584-5.60190.2155288250.215528825X-RAY DIFFRACTION89
5.6019-5.89680.2155291710.215529171X-RAY DIFFRACTION90
5.8968-6.26560.2195295990.219529599X-RAY DIFFRACTION91
6.2656-6.74830.2248298950.224829895X-RAY DIFFRACTION92
6.7483-7.42550.238300920.23830092X-RAY DIFFRACTION92
7.4255-8.49540.2343299630.234329963X-RAY DIFFRACTION92
8.4954-10.68610.2181299610.218129961X-RAY DIFFRACTION91
10.6861-49.96420.2664296620.266429662X-RAY DIFFRACTION88

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