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- PDB-9lgj: Cryo-EM structure of a designed AAV2-based vector -

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Basic information

Entry
Database: PDB / ID: 9lgj
TitleCryo-EM structure of a designed AAV2-based vector
ComponentsCapsid protein VP1
KeywordsVIRUS / AAV2 / Adeno-associated Virus Serotype 2 mutant
Function / homology
Function and homology information


symbiont entry into host cell via permeabilization of host 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 VP1/VP2 / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
Biological speciesAdeno-associated virus 2 Srivastava/1982
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.58 Å
AuthorsLuo, S. / Ke, X. / Zheng, Q.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Cryo-EM structure of a designed AAV2-based vector
Authors: Luo, S. / Ke, X. / Zheng, Q.
History
DepositionJan 10, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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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
V: Capsid protein VP1
W: Capsid protein VP1
X: Capsid protein VP1
Y: Capsid protein VP1
Z: Capsid protein VP1
AA: Capsid protein VP1
BA: Capsid protein VP1
CA: Capsid protein VP1
DA: Capsid protein VP1
EA: Capsid protein VP1
FA: Capsid protein VP1
GA: Capsid protein VP1
HA: Capsid protein VP1
IA: Capsid protein VP1
JA: Capsid protein VP1
KA: Capsid protein VP1
LA: Capsid protein VP1
MA: Capsid protein VP1
NA: Capsid protein VP1
OA: Capsid protein VP1
PA: Capsid protein VP1
QA: Capsid protein VP1
RA: Capsid protein VP1
SA: Capsid protein VP1
TA: Capsid protein VP1
UA: Capsid protein VP1
VA: Capsid protein VP1
WA: Capsid protein VP1
XA: Capsid protein VP1
YA: Capsid protein VP1
ZA: Capsid protein VP1
AB: Capsid protein VP1
BB: Capsid protein VP1
CB: Capsid protein VP1
DB: Capsid protein VP1
EB: Capsid protein VP1
FB: Capsid protein VP1
GB: Capsid protein VP1
HB: Capsid protein VP1
IB: Capsid protein VP1


Theoretical massNumber of molelcules
Total (without water)4,971,13060
Polymers4,971,13060
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Capsid protein VP1


Mass: 82852.172 Da / Num. of mol.: 60 / Mutation: I204T, V716I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus 2 Srivastava/1982
Gene: VP1 / Production host: Homo sapiens (human) / References: UniProt: P03135
Has protein modificationN

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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: AAV2 mutant / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: adeno-associated virus 2
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 10000 nm / Nominal defocus min: 5000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19555 / Symmetry type: POINT

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