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- EMDB-7452: Atomic structure of a rationally engineered gene delivery vector,... -

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Basic information

Entry
Database: EMDB / ID: EMD-7452
TitleAtomic structure of a rationally engineered gene delivery vector, AAV2.5
Map datarationally engineered gene delivery vector, AAV2.5
SampleAAV2.5 != Adeno-associated virus 2

AAV2.5

  • Virus: Adeno-associated virus 2
    • Protein or peptide: Capsid protein VP1
KeywordsAAV / dependoparvovirus / gene therapy vector / retional design / VIRUS
Function / homology
Function and homology information


symbiont entry into host cell via permeabilization of host membrane / host cell nucleolus / T=1 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / structural molecule activity
Similarity search - Function
Phospholipase 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
Similarity search - Domain/homology
Biological speciesAdeno-associated virus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsBurg M / Rosebrough C
CitationJournal: J Struct Biol / Year: 2018
Title: Atomic structure of a rationally engineered gene delivery vector, AAV2.5.
Authors: Matthew Burg / Claire Rosebrough / Lauren M Drouin / Antonette Bennett / Mario Mietzsch / Paul Chipman / Robert McKenna / Duncan Sousa / Mark Potter / Barry Byrne / R Jude Samulski / Mavis Agbandje-McKenna /
Abstract: AAV2.5 represents the first structure-guided in-silico designed Adeno-associated virus (AAV) gene delivery vector. This engineered vector combined the receptor attachment properties of AAV serotype 2 ...AAV2.5 represents the first structure-guided in-silico designed Adeno-associated virus (AAV) gene delivery vector. This engineered vector combined the receptor attachment properties of AAV serotype 2 (AAV2) with the muscle tropic properties of AAV1, and exhibited an antibody escape phenotype because of a modified antigenic epitope. To confirm the design, the structure of the vector was determined to a resolution of 2.78 Å using cryo-electron microscopy and image reconstruction. The structure of the major viral protein (VP), VP3, was ordered from residue 219 to 736, as reported for other AAV structures, and the five AAV2.5 residues exchanged from AAV2 to AAV1, Q263A, T265 (insertion), N706A, V709A, and T717N, were readily interpretable. Significantly, the surface loops containing these residues adopt the AAV1 conformation indicating the importance of amino acid residues in dictating VP structure.
History
DepositionFeb 2, 2018-
Header (metadata) releaseMar 7, 2018-
Map releaseMay 30, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6cbe
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6cbe
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7452.png

Downloads & links

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Map

FileDownload / File: emd_7452.map.gz / Format: CCP4 / Size: 242.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationrationally engineered gene delivery vector, AAV2.5
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.95 Å/pix.
x 399 pix.
= 379.05 Å		0.95 Å/pix.
x 399 pix.
= 379.05 Å		0.95 Å/pix.
x 399 pix.
= 379.05 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-8.73986 - 16.7774
Average (Standard dev.)-0.000000000157065 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-199-199-199
Dimensions399399399
Spacing399399399
CellA=B=C: 379.05 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.950.950.95
M x/y/z399399399
origin x/y/z0.0000.0000.000
length x/y/z379.050379.050379.050
α/β/γ90.00090.00090.000
start NX/NY/NZ-199-199-199
NX/NY/NZ399399399
MAP C/R/S213
start NC/NR/NS-199-199-199
NC/NR/NS399399399
D min/max/mean-8.74016.777-0.000

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Supplemental data

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Sample components

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Entire : AAV2.5

EntireName: AAV2.5
Components
  • Virus: Adeno-associated virus 2
    • Protein or peptide: Capsid protein VP1

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Supramolecule #1: Adeno-associated virus 2

SupramoleculeName: Adeno-associated virus 2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10804 / Sci species name: Adeno-associated virus 2 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Adeno-associated virus 2
Molecular weightTheoretical: 82.017328 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAADGYLPDW LEDTLSEGIR QWWKLKPGPP PPKPAERHKD DSRGLVLPGY KYLGPFNGLD KGEPVNEADA AALEHDKAYD RQLDSGDNP YLKYNHADAE FQERLKEDTS FGGNLGRAVF QAKKRVLEPL GLVEEPVKTA PGKKRPVEHS PVEPDSSSGT G KAGQQPAR ...String:
MAADGYLPDW LEDTLSEGIR QWWKLKPGPP PPKPAERHKD DSRGLVLPGY KYLGPFNGLD KGEPVNEADA AALEHDKAYD RQLDSGDNP YLKYNHADAE FQERLKEDTS FGGNLGRAVF QAKKRVLEPL GLVEEPVKTA PGKKRPVEHS PVEPDSSSGT G KAGQQPAR KRLNFGQTGD ADSVPDPQPL GQPPAAPSGL GTNTMATGSG APMADNNEGA DGVGNSSGNW HCDSTWMGDR VI TTSTRTW ALPTYNNHLY KQISSASTGA SNDNHYFGYS TPWGYFDFNR FHCHFSPRDW QRLINNNWGF RPKRLNFKLF NIQ VKEVTQ NDGTTTIANN LTSTVQVFTD SEYQLPYVLG SAHQGCLPPF PADVFMVPQY GYLTLNNGSQ AVGRSSFYCL EYFP SQMLR TGNNFTFSYT FEDVPFHSSY AHSQSLDRLM NPLIDQYLYY LSRTNTPSGT TTQSRLQFSQ AGASDIRDQS RNWLP GPCY RQQRVSKTSA DNNNSEYSWT GATKYHLNGR DSLVNPGPAM ASHKDDEEKF FPQSGVLIFG KQGSEKTNVD IEKVMI TDE EEIRTTNPVA TEQYGSVSTN LQRGNRQAAT ADVNTQGVLP GMVWQDRDVY LQGPIWAKIP HTDGHFHPSP LMGGFGL KH PPPQILIKNT PVPANPSTTF SAAKFASFIT QYSTGQVSVE IEWELQKENS KRWNPEIQYT SNYAKSANVD FTVDNNGV Y SEPRPIGTRY LTRNL

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 TITAN KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Average electron dose: 2.0 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

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Auto3DEM (ver. 4.05.2) / Number images used: 24618
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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