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- EMDB-44196: RhAAV4282 Empty Capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-44196
TitleRhAAV4282 Empty Capsid
Map dataMain Map
Sample
  • Virus: Adeno-associated virus
    • Protein or peptide: Capsid protein VP1
KeywordsAAV / Adeno-Associated Virus / Empty Capsid / VIRAL PROTEIN
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
Methodsingle particle reconstruction / cryo EM / Resolution: 2.57 Å
AuthorsDagotto G / Jenni S / Li Z / Barouch DH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorOD011170 United States
CitationJournal: Mol Ther Methods Clin Dev / Year: 2024
Title: Identification of a novel neutralization epitope in rhesus AAVs.
Authors: Gabriel Dagotto / Jana L Fisher / David Li / Zhenyu Li / Simon Jenni / Zongli Li / Lawrence J Tartaglia / Peter Abbink / Dan H Barouch /
Abstract: Adeno-associated viruses (AAVs) are popular gene therapy delivery vectors, but their application can be limited by anti-vector immunity. Both preexisting neutralizing antibodies (NAbs) and post- ...Adeno-associated viruses (AAVs) are popular gene therapy delivery vectors, but their application can be limited by anti-vector immunity. Both preexisting neutralizing antibodies (NAbs) and post-administration NAbs can limit transgene expression and reduce the clinical utility of AAVs. The development of novel AAVs will advance our understanding of AAV immunity and may also have practical applications. In this study, we identified five novel AAV capsids from rhesus macaques. RhAAV4282 exhibited 91.4% capsid sequence similarity with AAV7 and showed similar tissue tropism with slightly diminished overall signal. Despite this sequence homology, RhAAV4282 and AAV7 showed limited cross-neutralization. We determined a cryo-EM structure of the RhAAV4282 capsid at 2.57 Å resolution and identified a small segment within the hypervariable region IV, involving seven amino acids that formed a shortened external loop in RhAAV4282 compared with AAV7. We generated RhAAV4282 and AAV7 mutants that involved swaps of this region and showed that this region partially determined neutralization phenotype. We termed this region the hypervariable region IV neutralizing epitope (HRNE). Our data suggests that modification of the HRNE can lead to AAVs with altered neutralization profiles.
History
DepositionMar 22, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44196.png

Downloads & links

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Map

FileDownload / File: emd_44196.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 384 pix.
= 472.32 Å		1.23 Å/pix.
x 384 pix.
= 472.32 Å		1.23 Å/pix.
x 384 pix.
= 472.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.23 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.035
Minimum - Maximum-0.12095609 - 0.17507449
Average (Standard dev.)0.00083415664 (±0.011120617)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 472.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unmodified map

Fileemd_44196_additional_1.map
AnnotationUnmodified map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_44196_half_map_1.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 1

Fileemd_44196_half_map_2.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Adeno-associated virus

EntireName: Adeno-associated virus
Components
  • Virus: Adeno-associated virus
    • Protein or peptide: Capsid protein VP1

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Supramolecule #1: Adeno-associated virus

SupramoleculeName: Adeno-associated virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Recombinant viral particles were grown using standard triple transfection method.
NCBI-ID: 272636 / Sci species name: Adeno-associated virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Macaca mulatta (Rhesus monkey)

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Adeno-associated virus
Molecular weightTheoretical: 58.137156 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DGVGNASGNW HCDSTWLGDR VITTSTRTWA LPTYNNHLYK QISSQSGATN DNHFFGYSTP WGYFDFNRFH CHFSPRDWQR LINNNWGFR PRKLRFKLFN IQVKEVTTND GVTTIANNLT STIQVFSDSE YQLPYVLGSA HQGCLPPFPA DVFMIPQYGY L TLNNGSQS ...String:
DGVGNASGNW HCDSTWLGDR VITTSTRTWA LPTYNNHLYK QISSQSGATN DNHFFGYSTP WGYFDFNRFH CHFSPRDWQR LINNNWGFR PRKLRFKLFN IQVKEVTTND GVTTIANNLT STIQVFSDSE YQLPYVLGSA HQGCLPPFPA DVFMIPQYGY L TLNNGSQS VGRSSFYCLE YFPSQMLRTG NNFEFSYTFE EVPFHSSYAH SQSLDRLMNP LIDQYLYYLA RTQSTTGSTR EL QFHQAGP NTMAEQSKNW LPGPCYRQQR LSKNIDSNNN SNFAWTGATK YHLNGRNSLT NPGVAMATNK DDEDQFFPIN GVL VFGKTG AANKTTLENV LMTSEEEIKT TNPVATEEYG VVSSNLQSST AGPQTQTVNS QGALPGMVWQ NRDVYLQGPI WAKI PHTDG NFHPSPLMGG FGLKHPPPQI LIKNTPVPAN PPEVFTPAKF ASFITQYSTG QVSVEIEWEL QKENSKRWNP EIQYT SNYA KSNNVEFAVN NEGVYTEPRP IGTRYLTRNL

UniProtKB: Capsid protein VP1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 52.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35328
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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