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- EMDB-29636: Cryo-EM Structure of AAV2-R404A Variant -

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Basic information

Entry
Database: EMDB / ID: EMD-29636
TitleCryo-EM Structure of AAV2-R404A Variant
Map data
Sample
  • Virus: adeno-associated virus 2
    • Protein or peptide: Capsid protein VP1
KeywordsSymmetry / capsid / AAV2 / 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 / adeno-associated virus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.62 Å
AuthorsBennett AD / McKenna R
Funding support United States, 2 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMS 1563234 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)GM082946 United States
CitationJournal: to be published
Title: Cryo-EM Structure of genome containing AAV2
Authors: Bennett AD / Mckenna R
History
DepositionJan 29, 2023-
Header (metadata) releaseJun 7, 2023-
Map releaseJun 7, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29636.png

Downloads & links

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Map

FileDownload / File: emd_29636.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.)
0.96 Å/pix.
x 400 pix.
= 384.8 Å		0.96 Å/pix.
x 400 pix.
= 384.8 Å		0.96 Å/pix.
x 400 pix.
= 384.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.962 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-7.118982 - 15.726895000000001
Average (Standard dev.)0.000000002103235 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 384.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_29636_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_29636_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : adeno-associated virus 2

EntireName: adeno-associated virus 2
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: SEROTYPE / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.9 MDa
Virus shellShell ID: 1 / Name: capsid / Diameter: 26.0 Å / T number (triangulation number): 1

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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
Molecular weightTheoretical: 56.722445 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GDRVITTSTR TWALPTYNNH LYKQISSQSG ASNDNHYFGY STPWGYFDFN RFHCHFSPRD WQRLINNNWG FRPKRLNFKL FNIQVKEVT QNDGTTTIAN NLTSTVQVFT DSEYQLPYVL GSAHQGCLPP FPADVFMVPQ YGYLTLNNGS QAVGRSSFYC L EYFPSQML ...String:
GDRVITTSTR TWALPTYNNH LYKQISSQSG ASNDNHYFGY STPWGYFDFN RFHCHFSPRD WQRLINNNWG FRPKRLNFKL FNIQVKEVT QNDGTTTIAN NLTSTVQVFT DSEYQLPYVL GSAHQGCLPP FPADVFMVPQ YGYLTLNNGS QAVGRSSFYC L EYFPSQML ATGNNFTFSY TFEDVPFHSS YAHSQSLDRL MNPLIDQYLY YLSRTNTPSG TTTQSRLQFS QAGASDIRDQ SR NWLPGPC YRQQRVSKTS ADNNNSEYSW TGATKYHLNG RDSLVNPGPA MASHKDDEEK FFPQSGVLIF GKQGSEKTNV DIE KVMITD EEEIRTTNPV ATEQYGSVST NLQRGNRQAA TADVNTQGVL PGMVWQDRDV YLQGPIWAKI PHTDGHFHPS PLMG GFGLK HPPPQILIKN TPVPANPSTT FSAAKFASFI TQYSTGQVSV EIEWELQKEN SKRWNPEIQY TSNYNKSVNV DFTVD TNGV YSEPRPIGTR YLTRNL

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

Concentration0.5 mg/mL
BufferpH: 7.3 / Component - Concentration: 1.0 mM / Component - Formula: PBS-MK / Component - Name: TD / Details: 1XPBS, 1 mM MgCl2, 2.5 mM KCl pH7.3
GridModel: Quantifoil / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Number real images: 1674 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
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: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 23783
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-8fzn:
Cryo-EM Structure of AAV2-R404A Variant

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