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- PDB-3ux1: Structural Characterization of Adeno-Associated Virus Serotype 9 -

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Basic information

Entry
Database: PDB / ID: 3ux1
TitleStructural Characterization of Adeno-Associated Virus Serotype 9
ComponentsCapsid protein VP1
KeywordsVIRUS / AAV9
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 9
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDiMattia, M.A. / Nam, H.-J. / Van Vliet, K. / Mitchell, M. / McCall, A. / Bennett, A. / Gurda, B. / McKenna, R. / Potter, M. / Sakai, Y. ...DiMattia, M.A. / Nam, H.-J. / Van Vliet, K. / Mitchell, M. / McCall, A. / Bennett, A. / Gurda, B. / McKenna, R. / Potter, M. / Sakai, Y. / Byrne, B.J. / Muzyczka, N. / Aslanidi, G. / Zolotukhin, S. / Olson, N. / Sinkovitis, R. / Baker, T.S. / Agbandje-McKenna, M.
CitationJournal: J.Virol. / Year: 2012
Title: Structural insight into the unique properties of adeno-associated virus serotype 9.
Authors: Dimattia, M.A. / Nam, H.J. / Van Vliet, K. / Mitchell, M. / Bennett, A. / Gurda, B.L. / McKenna, R. / Olson, N.H. / Sinkovits, R.S. / Potter, M. / Byrne, B.J. / Aslanidi, G. / Zolotukhin, S. ...Authors: Dimattia, M.A. / Nam, H.J. / Van Vliet, K. / Mitchell, M. / Bennett, A. / Gurda, B.L. / McKenna, R. / Olson, N.H. / Sinkovits, R.S. / Potter, M. / Byrne, B.J. / Aslanidi, G. / Zolotukhin, S. / Muzyczka, N. / Baker, T.S. / Agbandje-McKenna, M.
History
DepositionDec 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 13, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein VP1


Theoretical massNumber of molelcules
Total (without water)58,4741
Polymers58,4741
Non-polymers00
Water1,04558
1
A: Capsid protein VP1
x 60


Theoretical massNumber of molelcules
Total (without water)3,508,46560
Polymers3,508,46560
Non-polymers00
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
x 5


  • icosahedral pentamer
  • 292 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)292,3725
Polymers292,3725
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein VP1
x 6


  • icosahedral 23 hexamer
  • 351 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)350,8466
Polymers350,8466
Non-polymers00
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
x 60


  • crystal asymmetric unit, crystal frame
  • 3.51 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)3,508,46560
Polymers3,508,46560
Non-polymers00
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)250.680, 250.680, 632.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.36461, -0.85877, 0.35996), (0.64647, 0.51169, 0.56591), (-0.67017, 0.026366, 0.74173)36.751, 63.351, -30.182
3generate(-0.66346, -0.74305, -0.087746), (0.18724, -0.27843, 0.94203), (-0.72441, 0.60857, 0.32385)-15.117, 102.45, -75.528
4generate(-0.66346, 0.18724, -0.7244), (-0.74305, -0.27843, 0.60857), (-0.087746, 0.94203, 0.32385)-83.924, 63.255, -73.372
5generate(0.36461, 0.64647, -0.67018), (-0.85877, 0.51168, 0.026366), (0.35996, 0.56591, 0.74173)-74.582, -0.0589, -26.693
6generate(-0.91253, 0.14266, 0.38333), (0.14266, -0.76734, 0.62518), (0.38333, 0.62518, 0.67986)-91.119, 136.73, -30.092
7generate(-0.31725, -0.3, 0.89964), (0.93602, 0.053385, 0.34788), (-0.15239, 0.95245, 0.26387)-33.302, 109.45, -76.865
8generate(0.59156, 0.74738, 0.30247), (-0.71318, 0.31005, 0.62869), (0.37608, -0.58762, 0.71642)-72.484, 20.988, 59.305
9generate(-0.31725, 0.93602, -0.15239), (-0.29999, 0.053383, 0.95245), (0.89964, 0.34788, 0.26386)-124.72, 57.378, 12.168
10generate(-0.97435, 0.18762, 0.12426), (0.18762, 0.37238, 0.90892), (0.12426, 0.90892, -0.39803)-97.049, 54.325, -61.992
11generate(0.96352, -0.20528, -0.17172), (0.23033, 0.30926, 0.92266), (-0.1363, -0.92856, 0.34526)13.647, 60.793, 62.938
12generate(0.46579, 0.42066, -0.77851), (0.15052, 0.82929, 0.53816), (0.872, -0.36786, 0.32296)-53.618, 18.968, 63.942
13generate(0.35445, -0.6912, -0.62976), (0.87161, 0.48811, -0.045151), (0.3386, -0.53291, 0.77547)23.929, 74.579, 53.68
14generate(0.49613, -0.48093, -0.72289), (-0.11762, 0.78768, -0.60476), (0.86024, 0.38507, 0.33422)14.345, 10.749, 7.7585
15generate(-0.79844, -0.012121, -0.60195), (-0.012118, -0.99927, 0.036195), (-0.60195, 0.036194, 0.79772)-74.865, 147.36, -28.034
16generate(-0.49739, -0.86302, 0.088297), (0.86675, -0.49866, 0.008626), (0.036586, 0.080822, 0.99606)0.752, 147.36, -4.4365
17generate(0.59156, -0.71318, 0.37608), (0.74737, 0.31005, -0.58762), (0.30248, 0.62869, 0.71642)35.543, 82.515, -33.757
18generate(-0.49739, 0.86675, 0.036581), (-0.86302, -0.49866, 0.080821), (0.088294, 0.008629, 0.99606)-127.19, 74.49, 3.0813
19generate(0.96352, 0.23033, -0.1363), (-0.20528, 0.30926, -0.92856), (-0.17172, 0.92266, 0.34526)-18.573, 42.442, -75.477
20generate(-0.89863, -0.1245, 0.42067), (-0.1245, -0.8471, -0.51664), (0.42067, -0.51664, 0.74573)-70.774, 131.37, 55.934
21generate(-0.069311, -0.40657, 0.91099), (0.4961, -0.80631, -0.32211), (0.8655, 0.42961, 0.25758)-14.975, 154.5, 4.6848
22generate(0.35445, 0.87162, 0.3386), (-0.6912, 0.48811, -0.53291), (-0.62976, -0.04515, 0.77547)-91.662, 8.7433, -23.19
23generate(0.46579, 0.15053, 0.872), (0.42066, 0.82929, -0.36786), (-0.77851, 0.53816, 0.32295)-33.638, 30.348, -72.6
24generate(-0.069311, 0.4961, 0.8655), (-0.40657, -0.80631, 0.42961), (0.91099, -0.32211, 0.25758)-81.739, 116.47, 62.201
25generate(-0.13976, 0.69883, 0.7015), (0.69884, -0.43229, 0.56987), (0.7015, 0.56988, -0.42795)-99.702, 135.38, -12.598
26generate(0.49613, -0.11762, 0.86024), (-0.48093, 0.78768, 0.38506), (-0.72288, -0.60476, 0.33423)-12.527, -4.555, 14.277
27generate(-0.47165, -0.46357, 0.7501), (0.075796, 0.8262, 0.55826), (-0.87852, 0.32016, -0.35454)-27.708, 16.048, -60.689
28generate(-0.47166, 0.075795, -0.87852), (-0.46357, 0.8262, 0.32016), (0.7501, 0.55826, -0.35454)-67.601, -6.6734, -9.6918
29generate(0.10445, -0.67467, -0.73069), (0.66361, -0.49995, 0.55648), (-0.74075, -0.54302, 0.3955)12.175, 138.9, 8.9579
30generate(0.10445, 0.66361, -0.74075), (-0.67467, -0.49995, -0.54302), (-0.73069, 0.55648, 0.3955)-86.809, 82.52, -71.941
31generate(0.6518, 0.2627, 0.71144), (0.75737, -0.27415, -0.59265), (0.039357, 0.92511, -0.37765)-34.098, 126.15, -66.766
32generate(-0.28459, 0.33619, 0.89777), (-0.95741, -0.052099, -0.28399), (-0.048702, -0.94035, 0.3367)-78.981, 37.485, 67.5
33generate(0.7971, 0.063872, 0.60046), (0.063873, -0.99773, 0.021339), (0.60046, 0.021343, -0.79937)-13.271, 150.45, 23.716
34generate(0.26815, 0.9584, 0.097806), (0.29825, 0.013948, -0.95439), (-0.91605, 0.28509, -0.2821)-101.72, 85.495, -59.676
35generate(-0.69006, 0.7191, -0.081897), (-0.24678, -0.34016, -0.90741), (-0.68038, -0.60596, 0.41219)-124.38, 88.726, 16.157
36generate(0.90449, 0.1674, -0.39226), (-0.10182, -0.80839, -0.57977), (-0.41416, 0.56434, -0.71414)-16.404, 129.46, -59.187
37generate(-0.07048, -0.63601, 0.76845), (-0.63601, -0.56482, -0.5258), (0.76845, -0.52581, -0.3647)1.9461, 88.946, 71.262
38generate(0.7009, -0.70143, 0.12936), (-0.17117, -0.34148, -0.92417), (0.69242, 0.6256, -0.35941)39.28, 92.009, -17.103
39generate(0.33369, -0.33444, -0.88136), (-0.93701, -0.015234, -0.34898), (0.10328, 0.94229, -0.31846)-3.333, 35.617, -65.344
40generate(-0.2846, -0.95741, -0.048701), (0.33618, -0.0521, -0.94035), (0.89777, -0.28399, 0.33669)16.698, 91.979, 58.825
41generate(-0.55329, -0.76329, -0.33354), (-0.76329, 0.30425, 0.56993), (-0.33354, 0.56993, -0.75096)-8.9789, 19.306, -56.205
42generate(-0.48809, -0.19244, -0.85131), (0.44009, 0.78805, -0.43046), (0.75371, -0.58476, -0.29995)-48.455, 34.216, 75.002
43generate(-0.31914, -0.89578, -0.30941), (-0.67124, 0.44413, -0.59345), (0.66902, 0.01829, -0.74302)10.683, 12.838, 26.83
44generate(-0.69006, -0.24677, -0.68038), (0.7191, -0.34016, -0.60596), (-0.081899, -0.90741, 0.41218)-52.944, 129.42, 63.665
45generate(0.091617, -0.45418, -0.88618), (-0.45418, -0.81103, 0.36871), (-0.88619, 0.36871, -0.28059)-4.6742, 114.82, -64.603
46generate(0.90449, -0.10182, -0.41416), (0.1674, -0.80839, 0.56434), (-0.39226, -0.57978, -0.71414)3.5072, 140.81, 26.357
47generate(-0.31915, -0.67124, 0.66902), (-0.89577, 0.44413, 0.01829), (-0.30941, -0.59345, -0.74302)-5.9235, 3.378, 30.859
48generate(-0.62899, 0.69711, -0.3441), (0.69711, 0.30986, -0.64655), (-0.3441, -0.64655, -0.68086)-120.18, 80.412, 33.325
49generate(-0.95186, -0.24465, 0.18469), (-0.24465, 0.24332, -0.93858), (0.18469, -0.93858, -0.29146)-64.129, 45.66, 77.201
50generate(0.044835, 0.4484, -0.89271), (0.4484, -0.80757, -0.38311), (-0.89271, -0.38311, -0.23727)-73.403, 152.58, -9.2705
51generate(0.54152, -0.83977, -0.039231), (-0.83977, -0.54252, 0.021374), (-0.039233, 0.021371, -0.999)42.798, 78.714, -3.2334
52generate(-0.4881, 0.44009, 0.75371), (-0.19244, 0.78805, -0.58476), (-0.85131, -0.43046, -0.29995)-95.238, 7.5703, -4.0242
53generate(0.45193, 0.88779, -0.08714), (0.88779, -0.45716, -0.053279), (-0.087137, -0.053284, -0.99477)-88.752, 145.18, 0.2701
54generate(0.70089, -0.17117, 0.69242), (-0.70144, -0.34148, 0.6256), (0.12936, -0.92417, -0.35941)0.0603, 69.672, 73.804
55generate(0.6518, 0.75737, 0.039357), (0.26269, -0.27415, 0.92511), (0.71144, -0.59265, -0.37765)-70.686, 105.31, 73.805
56generate(-0.39858, 0.66422, 0.63241), (0.83117, 0.55308, -0.057042), (-0.38766, 0.50291, -0.77253)-108.04, 68.07, -53.528
57generate(-0.99866, -0.051754, 0.001495), (-0.051754, 0.997, -0.057541), (0.001488, -0.057541, -0.99834)-80.369, -1.9579, 4.3184
58generate(0.26815, 0.29825, -0.91605), (0.9584, 0.013952, 0.28509), (0.097809, -0.95439, -0.2821)-52.89, 113.31, 74.709
59generate(0.33369, -0.93701, 0.10329), (-0.33444, -0.015232, 0.9423), (-0.88136, -0.34898, -0.31845)41.235, 61.001, -11.317
60generate(-0.39858, 0.83117, -0.38766), (0.66422, 0.55308, 0.50291), (0.63241, -0.057039, -0.77253)-120.39, 61.037, 30.859

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Components

#1: Protein Capsid protein VP1


Mass: 58474.414 Da / Num. of mol.: 1 / Fragment: UNP Residues 219-736
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus 9 / Gene: cap / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6JC40
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.27 Å3/Da / Density % sol: 62.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: virus concentration of ~5 mg/ml in 30 mM HEPES, pH 7.3, with 30 mM MgCl, 100 mM NaCl, 200 mM (NH4)2SO4, 5% PEG6000, and 25% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2008 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 1039725 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 15.367
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.87 / Rsym value: 0.422

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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: PDB ENTRY 2QAO

2qao
PDB Unreleased entry


Resolution: 2.8→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2821 46424 random
Rwork0.2827 --
obs0.2841 932315 -
all-1039725 -
Refinement stepCycle: LAST / Resolution: 2.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4131 0 0 58 4189
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0074
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4531
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-ID
2.8-2.90.394832220.3929X-RAY DIFFRACTION
2.9-3.020.378138590.3778X-RAY DIFFRACTION
3.02-3.150.363545350.3625X-RAY DIFFRACTION
3.15-3.320.33549530.3365X-RAY DIFFRACTION
3.32-3.530.321349520.3197X-RAY DIFFRACTION
3.53-3.80.302349270.3004X-RAY DIFFRACTION
3.8-4.180.281849440.28X-RAY DIFFRACTION
4.18-4.790.249748330.2513X-RAY DIFFRACTION
4.79-6.030.237750160.2389X-RAY DIFFRACTION
6.03-400.198951830.2025X-RAY DIFFRACTION

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