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- PDB-6u3q: The atomic structure of a human adeno-associated virus capsid iso... -

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Basic information

Entry
Database: PDB / ID: 6u3q
TitleThe atomic structure of a human adeno-associated virus capsid isolate (AAVhu69/AAVv66)
ComponentsCapsid protein VP1
KeywordsVIRUS / adeno-associated virus / AAV
Function / homologyPhospholipase 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 / T=1 icosahedral viral capsid / structural molecule activity / Capsid protein VP1
Function and homology information
Biological speciesAdeno-associated virus
MethodELECTRON MICROSCOPY / single particle reconstruction / Resolution: 2.46 Å
AuthorsHsu, H.-L. / Brown, A. / Loveland, A. / Tai, P. / Korostelev, A. / Gao, G.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)2R01NS076991 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)5P01HL131471 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)5P01HD080642 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)5R01AI121135 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)UG3HL147367 United States
Department of Defense (DOD, United States)W81XWH-17-1-0212 United States
Bill & Melinda Gates FoundationOPP1132169 United States
CitationJournal: Nat Commun / Year: 2020
Title: Structural characterization of a novel human adeno-associated virus capsid with neurotropic properties.
Authors: Hung-Lun Hsu / Alexander Brown / Anna B Loveland / Anoushka Lotun / Meiyu Xu / Li Luo / Guangchao Xu / Jia Li / Lingzhi Ren / Qin Su / Dominic J Gessler / Yuquan Wei / Phillip W L Tai / ...Authors: Hung-Lun Hsu / Alexander Brown / Anna B Loveland / Anoushka Lotun / Meiyu Xu / Li Luo / Guangchao Xu / Jia Li / Lingzhi Ren / Qin Su / Dominic J Gessler / Yuquan Wei / Phillip W L Tai / Andrei A Korostelev / Guangping Gao /
Abstract: Recombinant adeno-associated viruses (rAAVs) are currently considered the safest and most reliable gene delivery vehicles for human gene therapy. Three serotype capsids, AAV1, AAV2, and AAV9, have ...Recombinant adeno-associated viruses (rAAVs) are currently considered the safest and most reliable gene delivery vehicles for human gene therapy. Three serotype capsids, AAV1, AAV2, and AAV9, have been approved for commercial use in patients, but they may not be suitable for all therapeutic contexts. Here, we describe a novel capsid identified in a human clinical sample by high-throughput, long-read sequencing. The capsid, which we have named AAVv66, shares high sequence similarity with AAV2. We demonstrate that compared to AAV2, AAVv66 exhibits enhanced production yields, virion stability, and CNS transduction. Unique structural properties of AAVv66 visualized by cryo-EM at 2.5-Å resolution, suggest that critical residues at the three-fold protrusion and at the interface of the five-fold axis of symmetry likely contribute to the beneficial characteristics of AAVv66. Our findings underscore the potential of AAVv66 as a gene therapy vector.
History
DepositionAug 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: 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
B: Capsid protein VP1
U: Capsid protein VP1
V: Capsid protein VP1
W: Capsid protein VP1
X: Capsid protein VP1
Y: Capsid protein VP1
Z: Capsid protein VP1
a: Capsid protein VP1
b: Capsid protein VP1
c: Capsid protein VP1
d: Capsid protein VP1
C: 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
D: 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
u: Capsid protein VP1
v: Capsid protein VP1
w: Capsid protein VP1
x: Capsid protein VP1
E: Capsid protein VP1
y: Capsid protein VP1
z: Capsid protein VP1
0: Capsid protein VP1
1: Capsid protein VP1
2: Capsid protein VP1
3: Capsid protein VP1
4: Capsid protein VP1
5: Capsid protein VP1
6: Capsid protein VP1
7: Capsid protein VP1
F: Capsid protein VP1
G: Capsid protein VP1
H: Capsid protein VP1
I: Capsid protein VP1
J: Capsid protein VP1


Theoretical massNumber of molelcules
Total (without water)4,909,38260
Polymers4,909,38260
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Capsid protein VP1 / AAVhu69 (AAVv66)


Mass: 81823.031 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Source: (natural) Adeno-associated virus / References: UniProt: Q670R6

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Adeno-associated virus / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Adeno-associated virus
Details of virusEmpty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION
Buffer solutionpH: 7 / Details: filtered through 0.22 um filter
Buffer component
IDConc.NameFormulaBuffer-ID
18 g/Lsodium chlorideNaCl1
20.2 g/Lpotassium chlorideKCl1
31.44 g/LDisodium phosphateNa2HPO41
40.24 g/LMonopotassium phosphateKH2PO41
550 g/LD-sorbitalC6H14O61
60.001 %pluronic acid F681
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 48.62 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.15.2_3472refinement
PHENIX1.15.2_3472refinement
EM softwareName: cisTEM / Version: 1.0.0 / Category: particle selection
CTF correctionType: NONE
Particle selectionNum. of particles selected: 52874
3D reconstructionResolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52874 / Symmetry type: POINT
RefinementStereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0085255660
ELECTRON MICROSCOPYf_angle_d0.549348780
ELECTRON MICROSCOPYf_chiral_restr0.044236480
ELECTRON MICROSCOPYf_plane_restr0.003346200
ELECTRON MICROSCOPYf_dihedral_angle_d12.3547149520

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