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- PDB-8fyw: Cryo-EM Structure of genome containing AAV2 -

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Basic information

Entry
Database: PDB / ID: 8fyw
TitleCryo-EM Structure of genome containing AAV2
ComponentsCapsid protein VP1
KeywordsVIRUS / capsid / genome / assembly / symmetry
Function / homology
Function and homology information


permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell nucleolus / T=1 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / 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 / Capsid protein VP1
Similarity search - Component
Biological speciesadeno-associated virus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsBennett, A.D. / Mckenna, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMS 1563234 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)GM082946 United States
CitationJournal: To Be Published
Title: Cryo-EM Structure of genome containing AAV2
Authors: Bennett, A.D. / Mckenna, R.
History
DepositionJan 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 2.0May 29, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id

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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
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
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
u: Capsid protein VP1
v: Capsid protein VP1
w: Capsid protein VP1
x: Capsid protein VP1
y: Capsid protein VP1
z: 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
8: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,941,754120
Polymers4,921,88160
Non-polymers19,87360
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Capsid protein VP1


Mass: 82031.352 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) adeno-associated virus 2 / Gene: VP1 / Production host: Baculoviridae (virus) / References: UniProt: P03135
#2: Chemical...
ChemComp-D5M / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE


Mass: 331.222 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: C10H14N5O6P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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 2 / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 3.9 MDa / Experimental value: NO
Source (natural)Organism: adeno-associated virus 2
Source (recombinant)Organism: Baculovirus expression vector pCTdual
Details of virusEmpty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: capsid / Diameter: 26 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.3 / Details: 1X PBS, 1 mM MgCl2, 2.5 mM KCl pH7.3
Buffer componentConc.: 1 mM / Name: TD / Formula: PBS-MK
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Num. of real images: 1674

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Processing

EM software
IDNameCategory
2Leginonimage acquisition
7UCSF Chimeramodel fitting
12cisTEM3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3838 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009258780
ELECTRON MICROSCOPYf_angle_d0.926352920
ELECTRON MICROSCOPYf_dihedral_angle_d9.481259920
ELECTRON MICROSCOPYf_chiral_restr0.05736720
ELECTRON MICROSCOPYf_plane_restr0.00746680

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