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- EMDB-21656: BatAAV-10HB - genome-containing particles -

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Basic information

Entry
Database: EMDB / ID: EMD-21656
TitleBatAAV-10HB - genome-containing particles
Map data
Sample
  • Virus: Adeno-associated virus
    • Protein or peptide: VP1 capsid
  • Ligand: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
KeywordsIcosahedral Capsid / AAV / Gene Therapy / non-primate / Bat / VIRUS
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 / VP1 capsid
Function and homology information
Biological speciesBat adeno-associated virus / Adeno-associated virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsMietzsch M / Agbandje-McKenna M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
CitationJournal: J Struct Biol / Year: 2020
Title: Structural characterization of a bat Adeno-associated virus capsid.
Authors: Mario Mietzsch / Ya Li / Justin Kurian / James Kennon Smith / Paul Chipman / Robert McKenna / Lin Yang / Mavis Agbandje-McKenna /
Abstract: Adeno-associated viruses (AAVs) are widespread among vertebrates. AAVs isolated from bats display low capsid protein sequence identities (<60%) to AAV2, AAV5, and other primate AAVs. Here we report the first capsid structure of a non-primate AAV which was isolated from bats. The capsid structure of BtAAV-10HB (10HB) was determined by cryo-electron microscopy and three-dimensional image reconstruction to 3.03 Å resolution. Comparison of empty and genome-containing capsids showed that the capsid structures are almost identical except for an ordered nucleotide in a previously described nucleotide-binding pocket, the density in the 5-fold channel, and several amino acids with altered side chain conformations. Compared to other dependoparvoviruses, for example AAV2 and AAV5, 10HB displays unique structural features including insertions and deletions in capsid surface loops. Overall, the 10HB capsid structure superposes with an RMSD of 1.7 Å and 1.8 Å to AAV2 and AAV5, respectively. Currently all approved AAV human gene therapy biologics and vectors in clinical trials are based on primate isolates. However, pre-existing neutralizing antibodies in the human population represents a hurdle to their use. 10HB capsids are capable of packaging AAV2 vector genomes and thus have potential as gene delivery vectors. Significantly, a screen with human sera showed lack of recognition by the 10HB capsid. Thus, the different capsid surface of 10HB vectors likely renders it "invisible" to potential pre-existing neutralizing human anti-AAV antibodies especially because this virus or similar variants do not exist in primate populations.
History
DepositionApr 4, 2020-
Header (metadata) releaseJun 24, 2020-
Map releaseJun 24, 2020-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wft
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6wft
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21656.png

Downloads & links

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Map

FileDownload / File: emd_21656.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.06 Å/pix.
x 400 pix.
= 425.6 Å		1.06 Å/pix.
x 400 pix.
= 425.6 Å		1.06 Å/pix.
x 400 pix.
= 425.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.064 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 3
Minimum - Maximum-7.9515576 - 13.25752
Average (Standard dev.)-0.000000008089142 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 425.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0641.0641.064
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z425.600425.600425.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ400400400
MAP C/R/S213
start NC/NR/NS-200-200-200
NC/NR/NS400400400
D min/max/mean-7.95213.258-0.000

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Supplemental data

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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: VP1 capsid
  • Ligand: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE

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Supramolecule #1: Adeno-associated virus

SupramoleculeName: Adeno-associated virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 272636 / Sci species name: Adeno-associated virus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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Macromolecule #1: VP1 capsid

MacromoleculeName: VP1 capsid / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Bat adeno-associated virus
Molecular weightTheoretical: 57.741039 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DGVGQSSGNW HCDSVWMGDR VLTKSTRTWS LPTYNNHLYK QINGSGTGDA VYFGYSTPWG YFDFNRFHCH FSPRDWQRLV NNHWGIRPR RLNFKLFNIQ VKEVTTTDGT KTIANNLTST VQVFADTEHQ LPYILGSAHE GCMPPFPADV FMLPQYGYLT L NGPGSNNN ...String:
DGVGQSSGNW HCDSVWMGDR VLTKSTRTWS LPTYNNHLYK QINGSGTGDA VYFGYSTPWG YFDFNRFHCH FSPRDWQRLV NNHWGIRPR RLNFKLFNIQ VKEVTTTDGT KTIANNLTST VQVFADTEHQ LPYILGSAHE GCMPPFPADV FMLPQYGYLT L NGPGSNNN NLSTPSSAFY CLEYFPSQML RTGNNFVFTY EFEKVPFHSM FMHNQALDRL MNPLVDQYLW YLDATSGNNL TF RKAGAKN FPEYFRNWIP GPGCRNQQWN KVGTKNNPQT GTWASANKWR LQGRLNKYAP GQPNAPAEGF LTNAGDLAFA NAK ATGATT AAGTVPADIL LTSESETTTT NMMSNNGWGA IASNNQNASV APTVQYEDSA HVLPGMVWQD RDIYLQGPIW AKIP ETDGH FHPSPLMGGF GLKNPPPQIL IKNTPVPADP PTQFSSQKIN SFITQYSTGQ MTVEIEWELR KENSKRWNPE IQYTA NFNN SANAQFSVNN NGLYIEDRTI GTRYLTHTL

UniProtKB: VP1 capsid

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Macromolecule #2: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE

MacromoleculeName: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / type: ligand / ID: 2 / Number of copies: 60 / Formula: D5M
Molecular weightTheoretical: 331.222 Da
Chemical component information

ChemComp-D5M:
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE

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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 TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 75.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 4661
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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