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- PDB-9b7n: Fab2-4 in complex with the capsid of Adeno-associated virus type 9 -

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Basic information

Entry
Database: PDB / ID: 9b7n
TitleFab2-4 in complex with the capsid of Adeno-associated virus type 9
Components
  • Capsid protein VP1
  • Fab2-4 heavy chain
  • Fab2-4 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Adeno-associated virus / AAV / capsid / Fab-complex / antibody / NAb / VIRUS / VIRAL PROTEIN-IMMUNE SYSTEM complex
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
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsMietzsch, M. / McKenna, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural characterization of antibody-responses from Zolgensma treatment guides the design of a capsid suitable for redosing
Authors: Mietzsch, M. / Nelson, A.R. / Hsi, J. / Zachary, J. / Potts, L. / Chipman, P. / Ghanem, M. / Alexander, I.E. / Logan, G.J. / Huiskonen, J. / McKenna, R.
History
DepositionMar 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: 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
L: Fab2-4 light chain
H: Fab2-4 heavy chain


Theoretical massNumber of molelcules
Total (without water)384,1668
Polymers384,1668
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: 59873.875 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus / Strain: AAV9 / Gene: cap / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q6JC22
#2: Antibody Fab2-4 light chain


Mass: 11088.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Fab2-4 heavy chain


Mass: 13834.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
Has protein modificationY

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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: #1 / Source: MULTIPLE SOURCES
Source (natural)Organism: Adeno-associated virus
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Details of virusEmpty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION
Virus shellTriangulation number (T number): 1
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 360595 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00518881
ELECTRON MICROSCOPYf_angle_d0.74525699
ELECTRON MICROSCOPYf_dihedral_angle_d8.91114994
ELECTRON MICROSCOPYf_chiral_restr0.052653
ELECTRON MICROSCOPYf_plane_restr0.0053413

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