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- PDB-7l6a: The genome-containing AAV12 capsid -

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Basic information

Entry
Database: PDB / ID: 7l6a
TitleThe genome-containing AAV12 capsid
ComponentsVP1
KeywordsVIRUS / Icosahedral Capsid / AAV12 / Adeno-associated virus / Parvovirus / Gene Therapy
Function / homology
Function and homology information


T=1 icosahedral viral capsid / structural molecule activity
Similarity search - Function
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
Similarity search - Domain/homology
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / VP1
Similarity search - Component
Biological speciesAdeno-associated virus 12
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.67 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: Viruses / Year: 2021
Title: Completion of the AAV Structural Atlas: Serotype Capsid Structures Reveals Clade-Specific Features.
Authors: Mario Mietzsch / Ariana Jose / Paul Chipman / Nilakshee Bhattacharya / Nadia Daneshparvar / Robert McKenna / Mavis Agbandje-McKenna /
Abstract: The capsid structures of most Adeno-associated virus (AAV) serotypes, already assigned to an antigenic clade, have been previously determined. This study reports the remaining capsid structures of ...The capsid structures of most Adeno-associated virus (AAV) serotypes, already assigned to an antigenic clade, have been previously determined. This study reports the remaining capsid structures of AAV7, AAV11, AAV12, and AAV13 determined by cryo-electron microscopy and three-dimensional image reconstruction to 2.96, 2.86, 2.54, and 2.76 Å resolution, respectively. These structures complete the structural atlas of the AAV serotype capsids. AAV7 represents the first clade D capsid structure; AAV11 and AAV12 are of a currently unassigned clade that would include AAV4; and AAV13 represents the first AAV2-AAV3 hybrid clade C capsid structure. These newly determined capsid structures all exhibit the AAV capsid features including 5-fold channels, 3-fold protrusions, 2-fold depressions, and a nucleotide binding pocket with an ordered nucleotide in genome-containing capsids. However, these structures have viral proteins that display clade-specific loop conformations. This structural characterization completes our three-dimensional library of the current AAV serotypes to provide an atlas of surface loop configurations compatible with capsid assembly and amenable for future vector engineering efforts. Derived vectors could improve gene delivery success with respect to specific tissue targeting, transduction efficiency, antigenicity or receptor retargeting.
History
DepositionDec 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,532,846120
Polymers3,512,97360
Non-polymers19,87360
Water0
1


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

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Components

#1: Protein ...
VP1


Mass: 58549.543 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus 12 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: A9RAI0
#2: Chemical...
ChemComp-DA / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / Deoxyadenosine monophosphate


Type: DNA linking / Mass: 331.222 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: C10H14N5O6P / Comment: dAMP*YM
Has ligand of interestN

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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 12 / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Adeno-associated virus 12
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 FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10-2155_2155: / Classification: refinement
EM software
IDNameCategory
4cisTEMCTF correction
13cisTEM3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40764 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01258540
ELECTRON MICROSCOPYf_angle_d0.911353460
ELECTRON MICROSCOPYf_dihedral_angle_d8.065254580
ELECTRON MICROSCOPYf_chiral_restr0.06236720
ELECTRON MICROSCOPYf_plane_restr0.00746740

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