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- PDB-4iov: The structure of AAVrh32.33, a Novel Gene Delivery Vector -

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Basic information

Entry
Database: PDB / ID: 4iov
TitleThe structure of AAVrh32.33, a Novel Gene Delivery Vector
ComponentsCapsid protein VP1
KeywordsVIRUS / Beta Barrel Icosahedral capsid / viral capsid / plasma
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 VP1
Similarity search - Component
Biological speciesAdeno-associated virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsMikalism, K. / Nam, H.-J. / Van vilet, K. / Vandenberghe, L.H. / Mays, L.E. / McKenna, R. / Wilson, J. / Agbandje-McKenna, M.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: The structure of AAVrh32.33, a novel gene delivery vector.
Authors: Mikals, K. / Nam, H.J. / Van Vliet, K. / Vandenberghe, L.H. / Mays, L.E. / McKenna, R. / Wilson, J.M. / Agbandje-McKenna, M.
History
DepositionJan 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references
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

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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)81,4862
Polymers81,1551
Non-polymers3311
Water0
1
A: Capsid protein VP1
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)4,889,147120
Polymers4,869,27360
Non-polymers19,87360
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 VP1
hetero molecules
x 5


  • icosahedral pentamer
  • 407 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)407,42910
Polymers405,7735
Non-polymers1,6565
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein VP1
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 489 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)488,91512
Polymers486,9276
Non-polymers1,9876
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 VP1
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 4.89 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)4,889,147120
Polymers4,869,27360
Non-polymers19,87360
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)246.396, 247.521, 250.332
Angle α, β, γ (deg.)70.38, 65.37, 60.17
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1generate(1), (1), (1)
2generate(0.38174, 0.86508, 0.32542), (-0.62867, 0.50112, -0.59468), (-0.67753, 0.022429, 0.73516)0.0002, -0.0006
3generate(-0.61861, 0.77106, -0.15098), (-0.15213, -0.30607, -0.93978), (-0.77083, -0.55839, 0.30664)0.0001, 0.0004, 0.0001
4generate(-0.61861, -0.15214, -0.77083), (0.77106, -0.30607, -0.55838), (-0.15097, -0.93977, 0.30664)0.0006
5generate(0.38175, -0.62868, -0.67752), (0.86508, 0.50113, 0.022428), (0.32542, -0.59467, 0.73516)0.0004, 0.0002, -0.0003
6generate(-0.95496, -0.091491, 0.28226), (-0.091491, -0.81413, -0.57342), (0.28226, -0.57342, 0.7691)0.0002
7generate(-0.35185, 0.38666, 0.85246), (-0.92582, -0.009463, -0.37783), (-0.13803, -0.92217, 0.36131)-0.0004, -0.0002, -0.0004
8generate(0.54124, -0.77143, 0.3346), (0.77835, 0.30907, -0.54649), (0.31816, 0.55622, 0.76772)-0.0004, -0.0001, -0.0005
9generate(-0.35185, -0.92583, -0.13802), (0.38666, -0.009468, -0.92217), (0.85246, -0.37783, 0.36132)0.0005, 0.0005, -0.0001
10generate(-0.98015, -0.16068, 0.11615), (-0.16068, 0.30056, -0.94013), (0.11615, -0.94013, -0.32042)-0.0003, 0.0005
11generate(0.98349, 0.15389, -0.095188), (-0.13942, 0.30909, -0.94076), (-0.11535, 0.9385, 0.32544)-0.0003, 0.0004, -0.0004
12generate(0.4776, -0.48458, -0.73286), (-0.091974, 0.80199, -0.59022), (0.87375, 0.34929, 0.33846)0.0005, 0.0004, 0.0002
13generate(0.3871, 0.62247, -0.68021), (-0.86594, 0.49883, -0.036311), (0.31671, 0.60308, 0.73211)0.0005, -0.0003, -0.0002
14generate(0.4649, 0.47308, -0.74837), (0.089141, 0.81596, 0.57119), (0.88086, -0.33226, 0.33717)0.0002, -0.0002, -0.0004
15generate(-0.69848, 0.001446, -0.71563), (0.001445, -0.99999, -0.00343), (-0.71563, -0.00343, 0.69847)0.0001, -0.0001, -0.0006
16generate(-0.49827, 0.86541, -0.052834), (-0.86564, -0.49999, -0.02593), (-0.048856, 0.032815, 0.99827)0.0003, -0.0005
17generate(0.54124, 0.77835, 0.31816), (-0.77143, 0.30907, 0.55621), (0.33459, -0.54649, 0.76772)-0.0005, -0.0002, -0.0003
18generate(-0.49827, -0.86564, -0.048853), (0.86541, -0.49999, 0.032815), (-0.052832, -0.025927, 0.99827)-0.0001, -0.0005
19generate(0.98349, -0.13942, -0.11534), (0.15388, 0.3091, 0.9385), (-0.09519, -0.94076, 0.32545)0.0002, -0.0004, -0.0003
20generate(-0.959, 0.089668, 0.26883), (0.089665, -0.80388, 0.58799), (0.26883, 0.58799, 0.76288)-0.0001, -0.0001, -0.0006
21generate(-0.20104, 0.48797, 0.84939), (-0.46985, -0.80888, 0.35349), (0.85955, -0.32802, 0.39189)-0.0006, -0.0003, -0.0001
22generate(0.38709, -0.86594, 0.31671), (0.62247, 0.49883, 0.60308), (-0.68021, -0.036306, 0.73211)-0.0006, -0.0002
23generate(0.47759, -0.091975, 0.87375), (-0.48457, 0.80199, 0.34929), (-0.73287, -0.59022, 0.33845)-0.0006, 0.0002, 0.0002
24generate(-0.20104, -0.46985, 0.85955), (0.48797, -0.80888, -0.32802), (0.84939, 0.35349, 0.39189)-0.0005, 0.0002, 0.0001
25generate(-0.20348, -0.62022, 0.75758), (-0.62022, -0.51706, -0.5899), (0.75758, -0.5899, -0.27945)-0.0002, 0.0005, -0.0002
26generate(0.4649, 0.089142, 0.88087), (0.47309, 0.81596, -0.33226), (-0.74837, 0.57119, 0.33717)-0.0002, 0.0004, -0.0005
27generate(-0.47537, 0.4666, 0.74586), (-0.10727, 0.81071, -0.57554), (-0.87322, -0.3536, -0.33534)-0.0001
28generate(-0.47537, -0.10727, -0.87322), (0.4666, 0.81071, -0.3536), (0.74586, -0.57554, -0.33534)0.0001
29generate(0.2173, 0.63155, -0.74426), (-0.61957, -0.49995, -0.60513), (-0.75426, 0.59262, 0.28265)
30generate(0.2173, -0.61957, -0.75426), (0.63155, -0.49995, 0.59262), (-0.74426, -0.60513, 0.28265)0.0003, 0.0001
31generate(0.6218, -0.13419, 0.77159), (-0.76408, -0.32018, 0.56006), (0.1719, -0.9378, -0.30162)-0.0001, 0.0001
32generate(-0.36373, -0.39009, 0.84589), (0.91705, 0.009422, 0.39867), (-0.16349, 0.92073, 0.35431)0.0002
33generate(0.69823, 0.020839, 0.71557), (0.020838, -0.99974, 0.008782), (0.71557, 0.008779, -0.69849)-0.0004, 0.0002, 0.0003
34generate(0.37238, -0.917, 0.14296), (-0.38641, -0.013142, 0.92223), (-0.84381, -0.39866, -0.35923)0.0002, -0.0007, -0.0001
35generate(-0.60461, -0.77865, -0.16777), (0.14123, -0.31209, 0.9395), (-0.7839, 0.54433, 0.29867)0.0002, -0.0005, 0.0003
36generate(0.95678, -0.071698, -0.28183), (0.10957, -0.80881, 0.57777), (-0.26937, -0.58368, -0.766)-0.0004, -0.0003, 0.0005
37generate(-0.23136, 0.63052, 0.74089), (0.63052, -0.48278, 0.60776), (0.74089, 0.60776, -0.28586)-0.0002, -0.0005, -0.0001
38generate(0.60127, 0.78545, 0.14681), (0.15886, -0.29757, 0.94139), (0.7831, -0.5427, -0.30369)0.0001, -0.0004, 0.0004
39generate(0.3432, 0.38984, -0.85454), (0.92578, 0.013191, 0.37783), (0.15856, -0.92079, -0.35638)0.0003, -0.0003, 0.0007
40generate(-0.36373, 0.91705, -0.16349), (-0.39009, 0.009425, 0.92073), (0.84589, 0.39867, 0.3543)-0.0002, -0.0002, -0.0001
41generate(-0.55843, 0.76438, -0.32229), (0.76438, 0.3232, -0.55791), (-0.32229, -0.55791, -0.76477)0.0005, 0.0002
42generate(-0.46672, 0.074045, -0.8813), (-0.49117, 0.80698, 0.32791), (0.73548, 0.58591, -0.34026)0.0005, -0.0003, -0.0001
43generate(-0.40091, 0.85461, -0.33003), (0.61731, 0.51819, 0.59195), (0.6769, 0.033587, -0.73531)0.0002, -0.0001, 0.0006
44generate(-0.60461, 0.14123, -0.7839), (-0.77865, -0.31209, 0.54433), (-0.16777, 0.9395, 0.29866)0.0003, -0.0005, -0.0001
45generate(0.19017, 0.48778, -0.852), (0.48778, -0.80009, -0.34918), (-0.852, -0.34919, -0.39008)0.0005, 0.0001
46generate(0.95678, 0.10957, -0.26937), (-0.071696, -0.80882, -0.58368), (-0.28182, 0.57776, -0.76601)0.0005, 0.0002, 0.0003
47generate(-0.40091, 0.61732, 0.6769), (0.85461, 0.51819, 0.03359), (-0.33002, 0.59195, -0.73531)-0.0003, -0.0003, 0.0003
48generate(-0.5239, -0.78508, -0.33043), (-0.78507, 0.29457, 0.54487), (-0.33043, 0.54487, -0.77067)0.0001, 0.0001
49generate(-0.98668, 0.13244, 0.094423), (0.13244, 0.31715, 0.93908), (0.094427, 0.93908, -0.33047)-0.0003, -0.0003, 0.0003
50generate(0.21151, -0.46984, -0.85704), (-0.46984, -0.81779, 0.33237), (-0.85704, 0.33237, -0.39373)0.0005, 0.0001, 0.0002
51generate(0.47886, 0.87657, 0.04817), (0.87657, -0.48043, 0.028555), (0.048173, 0.028551, -0.99843)0.0002, 0.0002
52generate(-0.46672, -0.49117, 0.73548), (0.074042, 0.80699, 0.58591), (-0.8813, 0.32791, -0.34027)-0.0006, -0.0003, -0.0001
53generate(0.51744, -0.85405, 0.053458), (-0.85405, -0.51932, -0.030088), (0.053459, -0.030087, -0.99812)-0.0003, 0.0005
54generate(0.60126, 0.15887, 0.7831), (0.78545, -0.29757, -0.5427), (0.14681, 0.94139, -0.3037)-0.0003, 0.0004, 0.0003
55generate(0.6218, -0.76408, 0.1719), (-0.13419, -0.32018, -0.9378), (0.77159, 0.56006, -0.30162)0.0001, 0.0001, 0.0001
56generate(-0.36768, -0.63339, 0.6809), (-0.87603, 0.4816, -0.025058), (-0.31205, -0.6057, -0.73195)-0.0001, 0.0001, 0.0004
57generate(-0.99975, -0.022283, 5.9E-5), (-0.022283, 0.99974, -0.00535), (6.1E-5, -0.00535, -0.99999)0.0004, -0.0001, 0.0005
58generate(0.37238, -0.38641, -0.84381), (-0.917, -0.013148, -0.39866), (0.14295, 0.92223, -0.35924)0.0001, 0.0006, 0.0001
59generate(0.34319, 0.92578, 0.15856), (0.38984, 0.013187, -0.92079), (-0.85454, 0.37782, -0.35638)-0.0002, 0.0002, 0.0005
60generate(-0.36768, -0.87603, -0.31205), (-0.63339, 0.4816, -0.6057), (0.6809, -0.025057, -0.73195)0.0002, 0.0005
DetailsT=1 icosahedral virus

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Components

#1: Protein Capsid protein VP1 /


Mass: 81154.555 Da / Num. of mol.: 1 / Fragment: Adeno associated virus rh32-33 VP1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus / Strain: Adeno associated virus Rh32-33 / Gene: Adeno associated virus Rh32-33 VP1 / References: UniProt: B4Y891
#2: Chemical ChemComp-D5M / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / Deoxyadenosine monophosphate


Mass: 331.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O6P

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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: 1.3 mM KCl, 0.7 mM KH2PO4, 8.2 mM NaCl, 4 mM Na2HPO4, 5% glycerol, and 3.5% polyethylene glycol 8000 (PEG 8000) , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9125 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 9, 2009
RadiationMonochromator: Wiggler / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9125 Å / Relative weight: 1
ReflectionResolution: 3.5→40 Å / Num. all: 579942 / Num. obs: 397503 / % possible obs: 68.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Rsym value: 0.159 / Net I/σ(I): 2.98
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.65 / Rsym value: 0.387 / % possible all: 66

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→40 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.269 19875 Random
Rwork0.271 --
obs0.271 397503 -
all-580296 -
Refinement stepCycle: LAST / Resolution: 3.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4117 0 22 0 4139
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.63
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

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