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- EMDB-22412: Adeno-associated virus strain AAV7 capsid icosahedral structure -

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Basic information

Entry
Database: EMDB / ID: EMD-22412
TitleAdeno-associated virus strain AAV7 capsid icosahedral structure
Map data
Sample
  • Virus: Adeno-associated virus - 7
    • Protein or peptide: Capsid proteinCapsid
KeywordsAAV / parvovirus / Parvoviridae / adeno-associated virus / capsid / 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 / Capsid protein
Function and homology information
Biological speciesAdeno-associated virus - 7
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsFirlar E / Yost SA
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2020
Title: Structure of the AAVhu.37 capsid by cryoelectron microscopy.
Authors: Jason T Kaelber / Samantha A Yost / Keith A Webber / Emre Firlar / Ye Liu / Olivier Danos / Andrew C Mercer /
Abstract: Adeno-associated viruses (AAVs) are used as in vivo gene-delivery vectors in gene-therapy products and have been heavily investigated for numerous indications. Over 100 naturally occurring AAV ...Adeno-associated viruses (AAVs) are used as in vivo gene-delivery vectors in gene-therapy products and have been heavily investigated for numerous indications. Over 100 naturally occurring AAV serotypes and variants have been isolated from primate samples. Many reports have described unique properties of these variants (for instance, differences in potency, target cell or evasion of the immune response), despite high amino-acid sequence conservation. AAVhu.37 is of interest for clinical applications owing to its proficient transduction of the liver and central nervous system. The sequence identity of the AAVhu.37 VP1 to the well characterized AAVrh.10 serotype, for which no structure is available, is greater than 98%. Here, the structure of the AAVhu.37 capsid at 2.56 Å resolution obtained via single-particle cryo-electron microscopy is presented.
History
DepositionAug 7, 2020-
Header (metadata) releaseOct 7, 2020-
Map releaseOct 7, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.85
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.85
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7jot
  • Surface level: 0.85
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7jot
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22412.png

Downloads & links

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Map

FileDownload / File: emd_22412.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.72267 Å
Density
Contour LevelBy AUTHOR: 0.85 / Movie #1: 0.85
Minimum - Maximum-2.6185308 - 4.420671
Average (Standard dev.)0.020742014 (±0.24239412)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 390.24182 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.722670370370370.722670370370370.72267037037037
M x/y/z540540540
origin x/y/z0.0000.0000.000
length x/y/z390.242390.242390.242
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ510510510
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS540540540
D min/max/mean-2.6194.4210.021

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Supplemental data

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Mask #1

Fileemd_22412_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_22412_additional_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_22412_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_22412_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Adeno-associated virus - 7

EntireName: Adeno-associated virus - 7
Components
  • Virus: Adeno-associated virus - 7
    • Protein or peptide: Capsid proteinCapsid

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Supramolecule #1: Adeno-associated virus - 7

SupramoleculeName: Adeno-associated virus - 7 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Virions containing GFP-encoding ssDNA were assembled in transfected HEK293T helper cells.
NCBI-ID: 202812 / Sci species name: Adeno-associated virus - 7 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5 MDa
Virus shellShell ID: 1 / Diameter: 250.0 Å / T number (triangulation number): 1

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Adeno-associated virus - 7
Molecular weightTheoretical: 58.438547 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DGVGNASGNW HCDSTWLGDR VITTSTRTWA LPTYNNHLYK QISSETAGST NDNTYFGYST PWGYFDFNRF HCHFSPRDWQ RLINNNWGF RPKKLRFKLF NIQVKEVTTN DGVTTIANNL TSTIQVFSDS EYQLPYVLGS AHQGCLPPFP ADVFMIPQYG Y LTLNNGSQ ...String:
DGVGNASGNW HCDSTWLGDR VITTSTRTWA LPTYNNHLYK QISSETAGST NDNTYFGYST PWGYFDFNRF HCHFSPRDWQ RLINNNWGF RPKKLRFKLF NIQVKEVTTN DGVTTIANNL TSTIQVFSDS EYQLPYVLGS AHQGCLPPFP ADVFMIPQYG Y LTLNNGSQ SVGRSSFYCL EYFPSQMLRT GNNFEFSYSF EDVPFHSSYA HSQSLDRLMN PLIDQYLYYL ARTQSNPGGT AG NRELQFY QGGPSTMAEQ AKNWLPGPCF RQQRVSKTLD QNNNSNFAWT GATKYHLNGR NSLVNPGVAM ATHKDDEDRF FPS SGVLIF GKTGATNKTT LENVLMTNEE EIRPTNPVAT EEYGIVSSNL QAANTAAQTQ VVNNQGALPG MVWQNRDVYL QGPI WAKIP HTDGNFHPSP LMGGFGLKHP PPQILIKNTP VPANPPEVFT PAKFASFITQ YSTGQVSVEI EWELQKENSK RWNPE IQYT SNFEKQTGVD FAVDSQGVYS EPRPIGTRYL TRNL

UniProtKB: Capsid protein

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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
Component:
ConcentrationFormulaName
9.0 g/LNaClSodium chloridesodium chloride
0.144 g/LKH2PO4potassium phosphate dibasic
0.795 g/LNa2HPO4sodium phosphate monobasic

Details: PBS
GridModel: Quantifoil / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.286 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.037 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: LEICA EM GP / Details: Whatman #1 filter paper.
Detailsapprox. 8*10^14 genome copies per mL

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.836 µm / Calibrated defocus min: 0.244 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 130000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-30 / Number grids imaged: 1 / Number real images: 2430 / Average exposure time: 6.0 sec. / Average electron dose: 1.064 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 103227
Startup modelType of model: NONE
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1-beta)
Final 3D classificationSoftware - Name: RELION (ver. 3.1-beta)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1-beta)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1-beta) / Number images used: 71811
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6u95


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-7jot:
Adeno-associated virus strain AAV7 capsid icosahedral structure

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