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- EMDB-23204: The genome-containing AAV13 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-23204
TitleThe genome-containing AAV13 capsid
Map data
Sample
  • Virus: Adeno-associated virus 13
    • Protein or peptide: Capsid protein
  • Ligand: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
KeywordsIcosahedral Capsid / AAV13 / Adeno-associated virus / Parvovirus / Gene Therapy / VIRUS
Function / homologyPhospholipase 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 / T=1 icosahedral viral capsid / structural molecule activity / Capsid protein
Function and homology information
Biological speciesAdeno-associated virus 13
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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: Viruses / Year: 2021
Title: Completion of the AAV Structural Atlas: Serotype Capsid Structures Reveals Clade-Specific Features.
Authors: Mario Mietzsch / Ariana Jose / Paul Chipman / Nilakshee Bhattacharya / Nadia Daneshparvar / Robert McKenna / Mavis Agbandje-McKenna /
Abstract: The capsid structures of most Adeno-associated virus (AAV) serotypes, already assigned to an antigenic clade, have been previously determined. This study reports the remaining capsid structures of ...The capsid structures of most Adeno-associated virus (AAV) serotypes, already assigned to an antigenic clade, have been previously determined. This study reports the remaining capsid structures of AAV7, AAV11, AAV12, and AAV13 determined by cryo-electron microscopy and three-dimensional image reconstruction to 2.96, 2.86, 2.54, and 2.76 Å resolution, respectively. These structures complete the structural atlas of the AAV serotype capsids. AAV7 represents the first clade D capsid structure; AAV11 and AAV12 are of a currently unassigned clade that would include AAV4; and AAV13 represents the first AAV2-AAV3 hybrid clade C capsid structure. These newly determined capsid structures all exhibit the AAV capsid features including 5-fold channels, 3-fold protrusions, 2-fold depressions, and a nucleotide binding pocket with an ordered nucleotide in genome-containing capsids. However, these structures have viral proteins that display clade-specific loop conformations. This structural characterization completes our three-dimensional library of the current AAV serotypes to provide an atlas of surface loop configurations compatible with capsid assembly and amenable for future vector engineering efforts. Derived vectors could improve gene delivery success with respect to specific tissue targeting, transduction efficiency, antigenicity or receptor retargeting.
History
DepositionDec 23, 2020-
Header (metadata) releaseFeb 3, 2021-
Map releaseFeb 3, 2021-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7l6h
  • Surface level: 3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23204.png

Downloads & links

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Map

FileDownload / File: emd_23204.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.08 Å/pix.
x 420 pix.
= 453.6 Å		1.08 Å/pix.
x 420 pix.
= 453.6 Å		1.08 Å/pix.
x 420 pix.
= 453.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-10.492725999999999 - 16.336344
Average (Standard dev.)-0.000000001079111 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-210-210-210
Dimensions420420420
Spacing420420420
CellA=B=C: 453.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z453.600453.600453.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-210-210-210
NX/NY/NZ420420420
MAP C/R/S213
start NC/NR/NS-210-210-210
NC/NR/NS420420420
D min/max/mean-10.49316.336-0.000

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Supplemental data

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Sample components

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Entire : Adeno-associated virus 13

EntireName: Adeno-associated virus 13
Components
  • Virus: Adeno-associated virus 13
    • Protein or peptide: Capsid protein
  • Ligand: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE

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Supramolecule #1: Adeno-associated virus 13

SupramoleculeName: Adeno-associated virus 13 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 501327 / Sci species name: Adeno-associated virus 13 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Adeno-associated virus 13
Molecular weightTheoretical: 58.555508 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ADGVGNSSGN WHCDSQWLGD RVITTSTRTW ALPTYNNHLY KQISSQSGAT NDNHYFGYST PWGYFDFNRF HCHFSPRDWQ RLINNNWGF RPKRLNFKLF NIQVKEVTQN DGTTTIANNL TSTVQVFTDS EYQLPYVLGS AHQGCLPPFP ADVFMVPQYG Y LTLNNGSQ ...String:
ADGVGNSSGN WHCDSQWLGD RVITTSTRTW ALPTYNNHLY KQISSQSGAT NDNHYFGYST PWGYFDFNRF HCHFSPRDWQ RLINNNWGF RPKRLNFKLF NIQVKEVTQN DGTTTIANNL TSTVQVFTDS EYQLPYVLGS AHQGCLPPFP ADVFMVPQYG Y LTLNNGSQ AVGRSSFYCL EYFPSQMLRT GNNFQFSYTF EDVPFHSSYA HSQSLDRLMN PLIDQYLYYL NRTQTASGTQ QS RLLFSQA GPTSMSLQAK NWLPGPCYRQ QRLSKQANDN NNSNFPWTGA TKYHLNGRDS LVNPGPAMAS HKDDKEKFFP MHG TLIFGK EGTNANNADL ENVMITDEEE IRTTNPVATE QYGTVSNNLQ NSNAGPTTGT VNHQGALPGM VWQDRDVYLQ GPIW AKIPH TDGHFHPSPL MGGFGLKHPP PQIMIKNTPV PANPPTNFSA AKFASFITQY STGQVSVEIE WELQKENSKR WNPEI QYTS NYNKSVNVDF TVDTNGVYSE PRPIGTRYLT RNL

UniProtKB: Capsid protein

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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 K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cisTEM / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 6794
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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