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- EMDB-25903: Cryo-electron microscopy of Adeno-associated virus serotype 4 at 2.2 A -

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Basic information

Entry
Database: EMDB / ID: EMD-25903
TitleCryo-electron microscopy of Adeno-associated virus serotype 4 at 2.2 A
Map data
Sample
  • Virus: Adeno-associated virus
    • Protein or peptide: Capsid
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsAAV4 / adeno-associated virus / serotype 4 / VIRUS LIKE PARTICLE
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
Function and homology information
Biological speciesAdeno-associated virus - 4 / Adeno-associated virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.21 Å
AuthorsZane GM / Silveria MA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122564 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Cryo-EM structure of adeno-associated virus 4 at 2.2 Å resolution.
Authors: Grant Zane / Mark Silveria / Nancy Meyer / Tommi White / Rui Duan / Xiaoqin Zou / Michael Chapman /
Abstract: Adeno-associated virus (AAV) is the vector of choice for several approved gene-therapy treatments and is the basis for many ongoing clinical trials. Various strains of AAV exist (referred to as ...Adeno-associated virus (AAV) is the vector of choice for several approved gene-therapy treatments and is the basis for many ongoing clinical trials. Various strains of AAV exist (referred to as serotypes), each with their own transfection characteristics. Here, a high-resolution cryo-electron microscopy structure (2.2 Å) of AAV serotype 4 (AAV4) is presented. The receptor responsible for transduction of the AAV4 clade of AAV viruses (including AAV11, AAV12 and AAVrh32.33) is unknown. Other AAVs interact with the same cell receptor, adeno-associated virus receptor (AAVR), in one of two different ways. AAV5-like viruses interact exclusively with the polycystic kidney disease-like 1 (PKD1) domain of AAVR, while most other AAVs interact primarily with the PKD2 domain. A comparison of the present AAV4 structure with prior corresponding structures of AAV5, AAV2 and AAV1 in complex with AAVR provides a foundation for understanding why the AAV4-like clade is unable to interact with either PKD1 or PKD2 of AAVR. The conformation of the AAV4 capsid in variable regions I, III, IV and V on the viral surface appears to be sufficiently different from AAV2 to ablate binding with PKD2. Differences between AAV4 and AAV5 in variable region VII appear to be sufficient to exclude binding with PKD1.
History
DepositionJan 11, 2022-
Header (metadata) releaseJan 25, 2023-
Map releaseJan 25, 2023-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25903.png

Downloads & links

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Map

FileDownload / File: emd_25903.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.51 Å/pix.
x 600 pix.
= 304.793 Å		0.51 Å/pix.
x 600 pix.
= 304.793 Å		0.51 Å/pix.
x 600 pix.
= 304.793 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.50799 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.0523502 - 0.0798153
Average (Standard dev.)0.00024268485 (±0.006025739)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-300-300-300
Dimensions600600600
Spacing600600600
CellA=B=C: 304.793 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_25903_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_25903_half_map_2.map
Projections & Slices
AxesZYX

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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
  • Ligand: MAGNESIUM ION
  • Ligand: water

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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 / Sci species strain: Serotype 4 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.746 MDa
Virus shellShell ID: 1 / Name: Capsid / Diameter: 250.0 Å / T number (triangulation number): 1

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Macromolecule #1: Capsid

MacromoleculeName: Capsid / type: protein_or_peptide / ID: 1 / Details: VP1 sequence of AAV4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Adeno-associated virus - 4
Molecular weightTheoretical: 80.688023 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: TTDGYLPDWL EDNLSEGVRE WWALQPGAPK PKANQQHQDN ARGLVLPGYK YLGPGNGLDK GEPVNAADAA ALEHDKAYDQ QLKAGDNPY LKYNHADAEF QQRLQGDTSF GGNLGRAVFQ AKKRVLEPLG LVEQAGETAP GKKRPLIESP QQPDSSTGIG K KGKQPAKK ...String:
TTDGYLPDWL EDNLSEGVRE WWALQPGAPK PKANQQHQDN ARGLVLPGYK YLGPGNGLDK GEPVNAADAA ALEHDKAYDQ QLKAGDNPY LKYNHADAEF QQRLQGDTSF GGNLGRAVFQ AKKRVLEPLG LVEQAGETAP GKKRPLIESP QQPDSSTGIG K KGKQPAKK KLVFEDETGA GDGPPEGSTS GAMSDDSEMR AAAGGAAVEG GQGADGVGNA SGDWHCDSTW SEGHVTTTST RT WVLPTYN NHLYKRLGES LQSNTYNGFS TPWGYFDFNR FHCHFSPRDW QRLINNNWGM RPKAMRVKIF NIQVKEVTTS NGE TTVANN LTSTVQIFAD SSYELPYVMD AGQEGSLPPF PNDVFMVPQY GYCGLVTGNT SQQQTDRNAF YCLEYFPSQM LRTG NNFEI TYSFEKVPFH SMYAHSQSLD RLMNPLIDQY LWGLQSTTTG TTLNAGTATT NFTKLRPTNF SNFKKNWLPG PSIKQ QGFS KTANQNYKIP ATGSDSLIKY ETHSTLDGRW SALTPGPPMA TAGPADSKFS NSQLIFAGPK QNGNTATVPG TLIFTS EEE LAATNATDTD MWGNLPGGDQ SNSNLPTVDR LTALGAVPGM VWQNRDIYYQ GPIWAKIPHT DGHFHPSPLI GGFGLKH PP PQIFIKNTPV PANPATTFSS TPVNSFITQY STGQVSVQID WEIQKERSKR WNPEVQFTSN YGQQNSLLWA PDAAGKYT E PRAIGTRYLT HHL

UniProtKB: Capsid

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 219 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.33 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
25.0 mMHEPESHEPES
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: blot force: 4 time: 2 s.
DetailsThe sample was isolated by multiple rounds of cesium chloride density centrifugation and dialyzed into a HEPES-buffered, sodium chloride solution (see Meyer et al., 2019 Bioprotocols paper).

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 4809 / Average exposure time: 1.4 sec. / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 16500
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 75226
Startup modelType of model: OTHER
Details: Used an in-house model constructed by a colleague when they worked on AAV.Go, which was based on, the closely related, AAV5.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 75226
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final 3D classificationNumber classes: 1 / Avg.num./class: 75226 / Software - Name: RELION (ver. 3.1.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2g8g


Chain - Chain ID: A / Chain - Residue range: 211-734 / Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsLink to CNS_RSRef software: https://chapman.missouri.edu/software/
Output model

PDB-7thr:
Cryo-electron microscopy of Adeno-associated virus serotype 4 at 2.2 A

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