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- PDB-4rso: The structure of the neurotropic AAVrh.8 viral vector -

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Basic information

Entry
Database: PDB / ID: 4rso
TitleThe structure of the neurotropic AAVrh.8 viral vector
ComponentsCapsid protein VP1
KeywordsVIRUS / beta-barrel / capsid protein / icosahedral virus / adeno-associated virus / parvoviridae / dependoparvovirus / virus capsid protein / single-stranded DNA binding
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 protein
Similarity search - Component
Biological speciesNon-human primate Adeno-associated virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsHalder, S. / Van Vliet, K. / Smith, J.K. / McKenna, R. / Wilson, J.M. / Agbandje-McKenna, M.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Structure of neurotropic adeno-associated virus AAVrh.8.
Authors: Halder, S. / Van Vliet, K. / Smith, J.K. / Duong, T.T. / McKenna, R. / Wilson, J.M. / Agbandje-McKenna, M.
History
DepositionNov 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 28, 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 / 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
Revision 1.3Apr 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)81,8354
Polymers81,4461
Non-polymers3903
Water1086
1
A: Capsid protein VP1
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)4,910,119240
Polymers4,886,73960
Non-polymers23,380180
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 VP1
hetero molecules
x 5


  • icosahedral pentamer
  • 409 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)409,17720
Polymers407,2285
Non-polymers1,94815
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein VP1
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 491 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)491,01224
Polymers488,6746
Non-polymers2,33818
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 VP1
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 4.91 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)4,910,119240
Polymers4,886,73960
Non-polymers23,380180
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)355.500, 358.900, 371.500
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(0.31433, -0.66903, -0.6735), (0.74911, 0.61059, -0.25691), (0.58312, -0.42377, 0.69311)0.49256, -2.53418, -2.18697
3generate(-0.7951, -0.33339, -0.50662), (0.54306, -0.01948, -0.83947), (0.27, -0.94259, 0.19654)3.81562, -3.15045, -2.34248
4generate(-0.7951, 0.54306, 0.27), (-0.33339, -0.01948, -0.94259), (-0.50662, -0.83947, 0.19654)5.37693, -0.99711, -0.25057
5generate(0.31433, 0.74911, 0.58311), (-0.66903, 0.61059, -0.42377), (-0.6735, -0.25691, 0.69311)3.0188, 0.9492, 1.19691
6generate(-0.28411, 0.63012, -0.72266), (0.63012, -0.44538, -0.63607), (-0.72266, -0.63607, -0.27051)2.18221, -3.06508, -0.5108
7generate(-0.02416, 0.35757, -0.93357), (0.92443, 0.3635, 0.1153), (0.38058, -0.86024, -0.33934)1.05772, -2.34698, -3.61991
8generate(0.90683, 0.41934, 0.04256), (-0.11692, 0.34726, -0.93045), (-0.40495, 0.83879, 0.36394)0.38584, -1.5028, 0.02036
9generate(-0.02416, 0.92443, 0.38058), (0.35757, 0.3635, -0.86024), (-0.93357, 0.1153, -0.33934)3.57307, -2.63962, 0.03034
10generate(-0.88238, 0.44858, -0.14205), (0.44858, 0.71082, -0.54177), (-0.14205, -0.54177, -0.82844)4.83312, -2.24459, -3.08455
11generate(0.636, -0.66544, 0.39076), (0.71197, 0.31067, -0.62975), (0.29766, 0.67873, 0.67136)1.60527, -3.16755, -1.31097
12generate(0.38194, -0.03027, 0.92369), (0.44008, 0.88483, -0.15298), (-0.81268, 0.46493, 0.35127)3.36115, -1.47703, 1.03542
13generate(0.37297, -0.91462, 0.15612), (0.76361, 0.39815, 0.5083), (-0.52706, -0.07037, 0.84691)1.83963, -1.18345, 1.11634
14generate(0.62399, -0.31917, 0.71327), (-0.36868, 0.68455, 0.62885), (-0.68899, -0.65537, 0.30948)2.28332, 2.10779, 0.47207
15generate(-0.89385, 0.08165, -0.44087), (0.08165, -0.9372, -0.3391), (-0.44087, -0.3391, 0.83105)4.25883, -1.11601, 0.81918
16generate(-0.03867, -0.50648, -0.86139), (0.88106, -0.42396, 0.20973), (-0.47142, -0.75082, 0.46263)1.11099, -2.16553, 0.16077
17generate(0.90683, -0.11692, -0.40495), (0.41934, 0.34726, 0.83879), (0.04256, -0.93045, 0.36394)-0.51811, 0.34272, -1.4221
18generate(-0.03867, 0.88106, -0.47142), (-0.50648, -0.42396, -0.75082), (-0.86138, 0.20973, 0.46264)2.02587, -0.23498, 1.33677
19generate(0.636, 0.71197, 0.29766), (-0.66544, 0.31067, 0.67873), (0.39076, -0.62975, 0.67136)1.62382, 2.94203, -1.74134
20generate(0.05282, -0.10567, -0.993), (-0.10567, -0.98939, 0.09967), (-0.993, 0.09967, -0.06343)0.67756, 0.19103, 0.69862
21generate(0.75608, 0.23016, -0.61267), (0.56158, -0.70889, 0.42673), (-0.3361, -0.66671, -0.66523)-0.45168, -0.94795, -2.28038
22generate(0.37297, 0.76361, -0.52706), (-0.91462, 0.39815, -0.07037), (0.15612, 0.5083, 0.84691)0.80584, 2.23235, -0.6305
23generate(0.38194, 0.44008, -0.81268), (-0.03027, 0.88483, 0.46493), (0.92369, -0.15298, 0.35127)0.20742, 0.92644, -3.69444
24generate(0.75608, 0.56159, -0.3361), (0.23016, -0.70889, -0.66671), (-0.61267, 0.42673, -0.66523)0.10713, -2.0889, -1.38942
25generate(0.08831, 0.99564, -0.03005), (0.99564, -0.08914, -0.02749), (-0.03005, -0.02749, -0.99917)2.52053, -2.86537, -3.62925
26generate(0.624, -0.36868, -0.68899), (-0.31917, 0.68455, -0.65538), (0.71327, 0.62886, 0.30948)-0.32292, -0.40553, -3.10022
27generate(-0.4818, -0.35061, -0.80308), (0.03032, 0.90925, -0.41515), (0.87576, -0.22437, -0.42744)2.42565, -0.86329, -5.01931
28generate(-0.4818, 0.03032, 0.87576), (-0.35061, 0.90925, -0.22437), (-0.80308, -0.41516, -0.42744)5.59057, 0.50915, -0.55593
29generate(-0.47688, -0.87414, 0.09199), (0.83469, -0.48317, -0.26428), (0.27546, -0.04925, 0.96005)3.9989, -2.92824, -0.81755
30generate(-0.47688, 0.83469, 0.27546), (-0.87414, -0.48317, -0.04925), (0.09199, -0.26428, 0.96005)4.57644, 2.04052, -0.3568
31generate(0.49631, 0.86433, -0.0813), (0.36338, -0.12178, 0.92365), (0.78843, -0.48796, -0.37453)1.31646, 0.58446, -4.72433
32generate(0.46237, -0.02051, -0.88645), (-0.84746, -0.30429, -0.43499), (-0.26082, 0.95236, -0.15808)-0.20821, 1.27886, -1.3169
33generate(0.80906, 0.31777, 0.49442), (0.31776, -0.94418, 0.08685), (0.49442, 0.08685, -0.86487)1.47115, -0.95906, -4.76744
34generate(-0.3675, 0.92043, -0.13322), (-0.42637, -0.03944, 0.90369), (0.82653, 0.38891, 0.40694)3.53788, 2.67135, -3.2557
35generate(-0.64159, 0.32094, -0.69668), (-0.71627, -0.57566, 0.39444), (-0.27446, 0.75208, 0.59921)3.14366, 2.42834, 0.09543
36generate(0.04704, 0.48655, 0.87238), (-0.36473, -0.80468, 0.46846), (0.92992, -0.34022, 0.13961)4.23313, 1.5935, -4.12942
37generate(0.78066, -0.55677, -0.28385), (-0.55677, -0.82591, 0.08875), (-0.28385, 0.08875, -0.95475)-0.01698, 1.40041, -2.85188
38generate(0.88797, -0.10408, 0.44797), (-0.44428, -0.44584, 0.77707), (0.11885, -0.88904, -0.44213)1.1158, 2.42817, -3.11457
39generate(-0.07071, 0.08931, 0.99349), (-0.99741, -0.01976, -0.06921), (0.01345, -0.99581, 0.09047)4.71781, 2.39781, -1.86029
40generate(0.46237, -0.84746, -0.26082), (-0.02051, -0.30429, 0.95236), (-0.88645, -0.43499, -0.15808)0.83667, 1.63904, 0.16359
41generate(-0.76155, -0.5674, 0.3132), (-0.5674, 0.35017, -0.74527), (0.3132, -0.74527, -0.58862)5.2131, 0.04524, -3.88604
42generate(-0.38693, -0.74799, 0.53926), (0.05379, 0.56551, 0.82299), (-0.92054, 0.34744, -0.17858)4.60517, 1.32151, 0.32575
43generate(0.01561, -0.88511, 0.46511), (-0.91571, 0.17415, 0.36214), (-0.40153, -0.43156, -0.80779)3.37242, 3.00562, -2.33707
44generate(-0.64159, -0.71626, -0.27446), (0.32094, -0.57566, 0.75208), (-0.69668, 0.39444, 0.59921)3.78241, 0.31728, 1.17503
45generate(-0.75109, -0.25368, 0.60952), (-0.25368, -0.74145, -0.6212), (0.60952, -0.6212, 0.49254)5.77804, -0.71471, -2.65668
46generate(0.04704, -0.36473, 0.92992), (0.48655, -0.80468, -0.34022), (0.87238, 0.46846, 0.1396)4.22222, -2.18253, -3.86295
47generate(0.01561, -0.91571, -0.40153), (-0.88511, 0.17415, -0.43156), (0.46511, 0.36214, -0.80779)1.76118, 1.45264, -4.54493
48generate(-0.99971, 0.01813, 0.0161), (0.01813, 0.11806, 0.99284), (0.0161, 0.99284, -0.11835)5.38043, 1.66941, -1.97821
49generate(-0.33722, -0.74196, -0.57947), (-0.74196, -0.16941, 0.64869), (-0.57947, 0.64869, -0.49338)2.39896, 3.02458, -1.12881
50generate(-0.89828, 0.1082, 0.4259), (0.1082, -0.88491, 0.45301), (0.4259, 0.45301, 0.78319)5.8817, 0.28856, -1.47802
51generate(0.28382, -0.64825, 0.70656), (-0.64825, -0.67267, -0.35677), (0.70656, -0.35677, -0.61114)3.13507, 0.83996, -4.9258
52generate(-0.38693, 0.05379, -0.92054), (-0.74798, 0.56551, 0.34744), (0.53926, 0.82299, -0.17858)2.01016, 2.584, -3.51304
53generate(-0.29127, 0.67308, 0.6798), (0.67308, -0.36078, 0.6456), (0.6798, 0.6456, -0.34795)4.80688, -0.79213, -4.22747
54generate(0.88797, -0.44428, 0.11884), (-0.10408, -0.44584, -0.88904), (0.44797, 0.77707, -0.44213)0.45837, -1.57042, -3.76385
55generate(0.49631, 0.36338, 0.78843), (0.86433, -0.12178, -0.48796), (-0.0813, 0.92365, -0.37453)2.85909, -3.37196, -2.20219
56generate(-0.61811, 0.6818, -0.39125), (0.39111, 0.69848, 0.59929), (0.68188, 0.21741, -0.6984)3.69717, 0.023, -4.94212
57generate(-0.91521, -0.39941, -0.05356), (-0.39941, 0.88138, 0.25226), (-0.05355, 0.25226, -0.96618)4.96782, 1.51916, -3.4664
58generate(-0.3675, -0.42637, 0.82653), (0.92043, -0.03944, 0.38891), (-0.13322, 0.90369, 0.40694)5.13042, -1.88547, -0.61783
59generate(-0.07071, -0.99741, 0.01345), (0.08931, -0.01976, -0.99581), (0.99349, -0.06921, 0.09048)2.7503, -2.2264, -4.35297
60generate(-0.61811, 0.39111, 0.68188), (0.6818, 0.69848, 0.21741), (-0.39125, 0.59929, -0.6984)5.64596, -1.46239, -2.0191

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Components

#1: Protein Capsid protein VP1 /


Mass: 81445.648 Da / Num. of mol.: 1 / Fragment: Residues 217-736
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Non-human primate Adeno-associated virus
Gene: cap, VP1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q808Y3
#2: Chemical ChemComp-DA / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / Deoxyadenosine monophosphate


Type: DNA linking / Mass: 331.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O6P / Comment: dAMP*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Crystallization drops consisted of virus sample (10 mg/ml) in 1X PBS mixed with reservoir solution (5.5% PEG8000 in 1xPBS) at a 1:1 ratio (v/v) and equilibrated against 1 ml of reservoir ...Details: Crystallization drops consisted of virus sample (10 mg/ml) in 1X PBS mixed with reservoir solution (5.5% PEG8000 in 1xPBS) at a 1:1 ratio (v/v) and equilibrated against 1 ml of reservoir solution at 298K. pH 7.4; temperature 298K; hanging-drop vapor-diffusion, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9186 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 4, 2010 / Details: mirrors
RadiationMonochromator: White beam collimating mirror, horizontally focusing monochromator using single bent triangular Si(111) crystal, vertically focusing Rh-coated Si mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9186 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 532197 / Num. obs: 487416 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rsym value: 0.176 / Net I/σ(I): 3.2
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allRsym valueDiffraction-ID% possible all
3.5-3.632.1505450.371186
3.63-3.772376790.355164.2
3.77-3.942.1389150.339166.1
3.94-4.152.5554490.25194.3
4.15-4.412.7569960.226196.8
4.41-4.752.9579590.209198.2
4.75-5.233.1582460.183198.6
5.23-5.983.2585850.153198.9
5.98-7.533.3588060.113198.9
7.53-503.2590170.078197.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
CNS1.3refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AAV8 VP1

Resolution: 3.5→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.219 24216 random
Rwork0.217 --
all0.217 532197 -
obs0.217 487416 -
Refinement stepCycle: LAST / Resolution: 3.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4124 0 24 6 4154
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_bond_d0.008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-ID% reflection obs (%)
3.5-3.630.342321060.3379X-RAY DIFFRACTION73
3.63-3.770.334713620.3366X-RAY DIFFRACTION49.6
3.77-3.940.314415590.3077X-RAY DIFFRACTION54
3.94-4.150.248726220.2482X-RAY DIFFRACTION85.3
4.15-4.410.2126330.2143X-RAY DIFFRACTION89.4
4.41-4.750.204626940.1956X-RAY DIFFRACTION91.4
4.75-5.230.189526630.1854X-RAY DIFFRACTION93.3
5.23-5.980.165728200.17X-RAY DIFFRACTION94.7
5.98-7.530.153328570.1529X-RAY DIFFRACTION96.2
7.53-500.208929000.2041X-RAY DIFFRACTION96.8

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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