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- PDB-6wfu: BatAAV-10HB - empty particles -

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Basic information

Entry
Database: PDB / ID: 6wfu
TitleBatAAV-10HB - empty particles
ComponentsVP1 capsid
KeywordsVIRUS / Icosahedral Capsid / AAV / Gene Therapy / non-primate / Bat
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 / VP1 capsid
Function and homology information
Biological speciesBat adeno-associated virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsMietzsch, M. / Agbandje-McKenna, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
CitationJournal: J Struct Biol / Year: 2020
Title: Structural characterization of a bat Adeno-associated virus capsid.
Authors: Mario Mietzsch / Ya Li / Justin Kurian / James Kennon Smith / Paul Chipman / Robert McKenna / Lin Yang / Mavis Agbandje-McKenna /
Abstract: Adeno-associated viruses (AAVs) are widespread among vertebrates. AAVs isolated from bats display low capsid protein sequence identities (<60%) to AAV2, AAV5, and other primate AAVs. Here we report the first capsid structure of a non-primate AAV which was isolated from bats. The capsid structure of BtAAV-10HB (10HB) was determined by cryo-electron microscopy and three-dimensional image reconstruction to 3.03 Å resolution. Comparison of empty and genome-containing capsids showed that the capsid structures are almost identical except for an ordered nucleotide in a previously described nucleotide-binding pocket, the density in the 5-fold channel, and several amino acids with altered side chain conformations. Compared to other dependoparvoviruses, for example AAV2 and AAV5, 10HB displays unique structural features including insertions and deletions in capsid surface loops. Overall, the 10HB capsid structure superposes with an RMSD of 1.7 Å and 1.8 Å to AAV2 and AAV5, respectively. Currently all approved AAV human gene therapy biologics and vectors in clinical trials are based on primate isolates. However, pre-existing neutralizing antibodies in the human population represents a hurdle to their use. 10HB capsids are capable of packaging AAV2 vector genomes and thus have potential as gene delivery vectors. Significantly, a screen with human sera showed lack of recognition by the 10HB capsid. Thus, the different capsid surface of 10HB vectors likely renders it "invisible" to potential pre-existing neutralizing human anti-AAV antibodies especially because this virus or similar variants do not exist in primate populations.
History
DepositionApr 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.2Mar 6, 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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Assembly

Deposited unit
A: VP1 capsid
B: VP1 capsid
C: VP1 capsid
D: VP1 capsid
E: VP1 capsid
F: VP1 capsid
G: VP1 capsid
H: VP1 capsid
I: VP1 capsid
J: VP1 capsid
K: VP1 capsid
L: VP1 capsid
M: VP1 capsid
N: VP1 capsid
O: VP1 capsid
P: VP1 capsid
Q: VP1 capsid
R: VP1 capsid
S: VP1 capsid
T: VP1 capsid
U: VP1 capsid
V: VP1 capsid
W: VP1 capsid
X: VP1 capsid
Y: VP1 capsid
Z: VP1 capsid
a: VP1 capsid
b: VP1 capsid
c: VP1 capsid
d: VP1 capsid
e: VP1 capsid
f: VP1 capsid
g: VP1 capsid
h: VP1 capsid
i: VP1 capsid
j: VP1 capsid
k: VP1 capsid
l: VP1 capsid
m: VP1 capsid
n: VP1 capsid
o: VP1 capsid
p: VP1 capsid
q: VP1 capsid
r: VP1 capsid
s: VP1 capsid
t: VP1 capsid
u: VP1 capsid
v: VP1 capsid
w: VP1 capsid
x: VP1 capsid
y: VP1 capsid
z: VP1 capsid
1: VP1 capsid
2: VP1 capsid
3: VP1 capsid
4: VP1 capsid
5: VP1 capsid
6: VP1 capsid
7: VP1 capsid
8: VP1 capsid


Theoretical massNumber of molelcules
Total (without water)3,464,46260
Polymers3,464,46260
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
VP1 capsid


Mass: 57741.039 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bat adeno-associated virus / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: A0A2Z4K548

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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: RECOMBINANT
Source (natural)Organism: Adeno-associated virus
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 75 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10-2155_2155: / Classification: refinement
EM software
IDNameCategory
1cisTEMparticle selection
4cisTEMCTF correction
13cisTEM3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4088 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01252900
ELECTRON MICROSCOPYf_angle_d0.859345360
ELECTRON MICROSCOPYf_dihedral_angle_d9.729251520
ELECTRON MICROSCOPYf_chiral_restr0.05435700
ELECTRON MICROSCOPYf_plane_restr0.00645780

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