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- PDB-3kie: Crystal structure of adeno-associated virus serotype 3B -

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Basic information

Entry
Database: PDB / ID: 3kie
TitleCrystal structure of adeno-associated virus serotype 3B
ComponentsCapsid protein VP1
KeywordsVIRUS / capsid / parvovirus / icosahedral virus / beta barrel / single-stranded / dependovirus
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 VP1/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 3B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsLerch, T.F. / Xie, Q. / Chapman, M.S.
Citation
Journal: Virology / Year: 2010
Title: The structure of adeno-associated virus serotype 3B (AAV-3B): insights into receptor binding and immune evasion.
Authors: Lerch, T.F. / Xie, Q. / Chapman, M.S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Twinned crystals of adeno-associated virus serotype 3b prove suitable for structural studies
Authors: Lerch, T.F. / Xie, Q. / Ongley, H.M. / Hare, J. / Chapman, M.S.
History
DepositionNov 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 31, 2021Group: Derived calculations / Source and taxonomy / Category: entity_src_gen / struct_site
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1
D: Capsid protein VP1
E: Capsid protein VP1
F: Capsid protein VP1
G: Capsid protein VP1
H: Capsid protein VP1
I: Capsid protein VP1
J: Capsid protein VP1
K: Capsid protein VP1
L: Capsid protein VP1
M: Capsid protein VP1
N: Capsid protein VP1
O: Capsid protein VP1
P: Capsid protein VP1
Q: Capsid protein VP1
R: Capsid protein VP1
S: Capsid protein VP1
T: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,646,36940
Polymers1,639,74420
Non-polymers6,62420
Water00
1
A: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1
D: Capsid protein VP1
E: Capsid protein VP1
F: Capsid protein VP1
G: Capsid protein VP1
H: Capsid protein VP1
I: Capsid protein VP1
J: Capsid protein VP1
K: Capsid protein VP1
L: Capsid protein VP1
M: Capsid protein VP1
N: Capsid protein VP1
O: Capsid protein VP1
P: Capsid protein VP1
Q: Capsid protein VP1
R: Capsid protein VP1
S: Capsid protein VP1
T: Capsid protein VP1
hetero molecules

A: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1
D: Capsid protein VP1
E: Capsid protein VP1
F: Capsid protein VP1
G: Capsid protein VP1
H: Capsid protein VP1
I: Capsid protein VP1
J: Capsid protein VP1
K: Capsid protein VP1
L: Capsid protein VP1
M: Capsid protein VP1
N: Capsid protein VP1
O: Capsid protein VP1
P: Capsid protein VP1
Q: Capsid protein VP1
R: Capsid protein VP1
S: Capsid protein VP1
T: Capsid protein VP1
hetero molecules

A: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1
D: Capsid protein VP1
E: Capsid protein VP1
F: Capsid protein VP1
G: Capsid protein VP1
H: Capsid protein VP1
I: Capsid protein VP1
J: Capsid protein VP1
K: Capsid protein VP1
L: Capsid protein VP1
M: Capsid protein VP1
N: Capsid protein VP1
O: Capsid protein VP1
P: Capsid protein VP1
Q: Capsid protein VP1
R: Capsid protein VP1
S: Capsid protein VP1
T: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,939,106120
Polymers4,919,23360
Non-polymers19,87360
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)257.767, 257.767, 607.037
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O
161P
171Q
181R
191S
201T

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and resid 217:737A217 - 737
211chain B and resid 217:737B217 - 737
311chain C and resid 217:737C217 - 737
411chain D and resid 217:737D217 - 737
511chain E and resid 217:737E217 - 737
611chain F and resid 217:737F217 - 737
711chain G and resid 217:737G217 - 737
811chain H and resid 217:737H217 - 737
911chain I and resid 217:737I217 - 737
1011chain J and resid 217:737J217 - 737
1111chain K and resid 217:737K217 - 737
1211chain L and resid 217:737L217 - 737
1311chain M and resid 217:737M217 - 737
1411chain N and resid 217:737N217 - 737
1511chain O and resid 217:737O217 - 737
1611chain P and resid 217:737P217 - 737
1711chain Q and resid 217:737Q217 - 737
1811chain R and resid 217:737R217 - 737
1911chain S and resid 217:737S217 - 737
2011chain T and resid 217:737T217 - 737

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.932572, 0.015712, 0.360643), (-0.342804, 0.35161, 0.871123), (-0.113119, -0.936015, 0.333288)0.031061, 0.017853, 0.222557
3given(0.63781, 0.155111, -0.754413), (0.510368, 0.648468, 0.564813), (0.576821, -0.745272, 0.334435)-0.019586, 0.086037, 0.219233
4given(0.812007, -0.117642, -0.571668), (0.460497, -0.472649, 0.751363), (-0.35859, -0.873363, -0.329621)0.05743, 0.609369, 0.306198
5given(-0.481562, -0.130874, -0.866585), (0.44625, 0.814395, -0.370974), (0.754294, -0.565361, -0.333779)-0.039549, -0.089469, 0.079139
6given(-0.172063, -0.312916, -0.934065), (0.978369, -0.164824, -0.125008), (-0.11484, -0.93537, 0.334508)-0.119783, -0.365321, 0.134187
7given(0.327959, -0.819979, -0.469124), (0.691119, 0.546807, -0.472607), (0.644048, -0.169224, 0.746033)0.124122, -0.038679, 0.020494
8given(0.547961, -0.817711, -0.176316), (0.692374, 0.325076, 0.644161), (-0.469422, -0.475052, 0.744291)0.062718, -0.170568, 0.039905
9given(0.353888, -0.928236, 0.114631), (-0.352433, -0.018818, 0.935648), (-0.866345, -0.371515, -0.3338)0.13198, 0.101261, 0.03528
10given(-0.872098, 0.489331, 3.5E-5), (0.489331, 0.872098, 0.00051), (0.000219, 0.000462, -1)0.026661, 0.051759, 0.054473
11given(-0.805186, 0.470812, -0.360573), (0.46999, 0.135836, -0.872157), (-0.361643, -0.871714, -0.33065)0.262828, -0.213597, -0.075737
12given(0.051725, 0.760929, -0.646771), (0.983105, 0.075069, 0.166941), (0.175582, -0.644478, -0.74419)-0.22717, -0.131468, 0.082945
13given(0.325767, 0.691215, 0.645056), (-0.821487, 0.544676, -0.168784), (-0.468012, -0.474921, 0.745261)-0.069181, 0.041944, -0.011242
14given(-0.005563, -0.355329, 0.934725), (-0.933509, 0.336964, 0.122538), (-0.35851, -0.871893, -0.333578)0.054359, 0.033235, 0.207854
15given(0.355146, -0.347088, 0.867987), (0.007398, 0.929531, 0.368671), (-0.934781, -0.124511, 0.332687)-0.094256, 0.004959, 0.149658
16given(-0.877576, -0.445576, 0.176982), (-0.445706, 0.622194, -0.6436), (0.176656, -0.64369, -0.744618)0.13676, -0.071371, 0.015783
17given(-0.761129, -0.638071, -0.116399), (0.299384, -0.186421, -0.935744), (0.575372, -0.747069, 0.332919)0.280787, 0.314665, 0.131912
18given(-0.686628, -0.555645, 0.468828), (-0.335353, 0.814238, 0.473871), (-0.645042, 0.16815, -0.745417)0.068731, 0.066564, 0.135483
19given(-0.48231, 0.447772, 0.752912), (-0.127922, 0.814274, -0.56621), (-0.86661, -0.369403, -0.335453)-0.104286, 0.254659, 0.32565
20given(-0.76362, 0.296433, 0.573595), (-0.635672, -0.189465, -0.748347), (-0.113159, -0.936072, 0.333114)0.021411, 0.251974, 0.0893
DetailsThe biological assembly is a 60mer generated from the 20mer in the asymmetric unit by the operations: -0.5x-0.866y, 0.866x-0.5y, z and -0.5x+0.866y, -0.866x-0.5y, z

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Components

#1: Protein
Capsid protein VP1


Mass: 81987.219 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus 3B / Gene: Cap / Plasmid: pAAV3B / Cell line (production host): HeLa / Production host: Homo sapiens (human) / References: UniProt: O56139
#2: Chemical
ChemComp-D5M / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE


Mass: 331.222 Da / Num. of mol.: 20 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7.3
Details: 3.2-3.4% PEG 6000, 50mM magnesium chloride, 100mM hepes, pH 7.3, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9186 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 13, 2004
RadiationMonochromator: 0.916 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9186 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.172
ReflectionResolution: 3→100 Å / Num. all: 76529 / Num. obs: 76529 / % possible obs: 25.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 5.2
Reflection shellResolution: 3→3.07 Å / Redundancy: 1 % / Mean I/σ(I) obs: 1.92 / Num. unique all: 4081 / % possible all: 20.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
GLRFphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1lp3

1lp3


Resolution: 3→13.926 Å / Occupancy max: 1 / Occupancy min: 0.73 / σ(F): 1.96 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.262 2822 4.36 %thin shells
Rwork0.231 ---
all0.232 64782 --
obs0.231 64782 10.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.917 Å2 / ksol: 0.301 e/Å3
Displacement parametersBiso max: 198.24 Å2 / Biso mean: 105.875 Å2 / Biso min: 43.33 Å2
Baniso -1Baniso -2Baniso -3
1--20.301 Å2-0 Å20 Å2
2---20.301 Å20 Å2
3---32.148 Å2
Refinement stepCycle: LAST / Resolution: 3→13.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms83080 0 440 0 83520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00386120
X-RAY DIFFRACTIONf_angle_d0.694117620
X-RAY DIFFRACTIONf_chiral_restr0.04512200
X-RAY DIFFRACTIONf_plane_restr0.00315600
X-RAY DIFFRACTIONf_dihedral_angle_d15.97230480
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4176X-RAY DIFFRACTIONPOSITIONAL0.001
12B4176X-RAY DIFFRACTIONPOSITIONAL0.001
13C4176X-RAY DIFFRACTIONPOSITIONAL0.001
14D4176X-RAY DIFFRACTIONPOSITIONAL0.002
15E4176X-RAY DIFFRACTIONPOSITIONAL0.001
16F4176X-RAY DIFFRACTIONPOSITIONAL0.001
17G4176X-RAY DIFFRACTIONPOSITIONAL0.001
18H4176X-RAY DIFFRACTIONPOSITIONAL0.001
19I4176X-RAY DIFFRACTIONPOSITIONAL0.001
110J4176X-RAY DIFFRACTIONPOSITIONAL0.001
111K4176X-RAY DIFFRACTIONPOSITIONAL0.001
112L4176X-RAY DIFFRACTIONPOSITIONAL0.002
113M4176X-RAY DIFFRACTIONPOSITIONAL0.001
114N4176X-RAY DIFFRACTIONPOSITIONAL0.002
115O4176X-RAY DIFFRACTIONPOSITIONAL0.001
116P4176X-RAY DIFFRACTIONPOSITIONAL0.002
117Q4176X-RAY DIFFRACTIONPOSITIONAL0.002
118R4176X-RAY DIFFRACTIONPOSITIONAL0.001
119S4176X-RAY DIFFRACTIONPOSITIONAL0.001
120T4176X-RAY DIFFRACTIONPOSITIONAL0.001
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 98 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3-3.0510.3962968
3.051-3.1060.3893187
3.106-3.1650.3963111
3.165-3.2290.4393870.35694481
3.229-3.2980.3783353
3.298-3.3740.3623370
3.374-3.4570.353488
3.457-3.5490.3073340.32133133647
3.549-3.6520.313346
3.652-3.7670.2941486
3.767-3.8990.2821390.27539164055
3.899-4.0510.31920.25339424134
4.051-4.2310.2434302
4.231-4.4470.212028
4.447-4.7150.1892750.18840724347
4.715-5.0630.1784563
5.063-5.5430.2411860.19227352921
5.543-6.280.1884477
6.28-7.6850.1732935
7.685-13.9260.182690.13725142583

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