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- EMDB-74043: Cryo-EM structure of the engineered vector AAV2.ATX002 -

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Basic information

Entry
Database: EMDB / ID: EMD-74043
TitleCryo-EM structure of the engineered vector AAV2.ATX002
Map datastructure of the engineered vector AAV2.ATX002
Sample
  • Virus: adeno-associated virus 2
    • Protein or peptide: Engineered AAV2 capsid protein VP3
KeywordsAdeno-Associated Virus / AAV / Engineered AAV / 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 VP1/VP2 / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
Biological speciesadeno-associated virus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 1.9 Å
AuthorsBetegon M / Byrne LC / Conway JF
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)UH3MH120094 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)UF1MH130881 United States
National Institutes of Health/National Eye Institute (NIH/NEI)P30 EY08098 United States
National Institutes of Health/Office of the DirectorS10OD019995 United States
National Institutes of Health/Office of the DirectorS10OD025009 United States
CitationJournal: To Be Published
Title: Structural dynamics insights into principles underlying the increased fitness of newly engineered and broadly potent AAV capsids
Authors: Johnson ME / Ozturk BE / Tugwell TH / Lambros M / Janowitz H / Sedorovitz M / Flohr K / Campello L / Hartung JE / Hogle B / Gillespie M / Schriever H / Aweidah H / Koester J / Clausen I / ...Authors: Johnson ME / Ozturk BE / Tugwell TH / Lambros M / Janowitz H / Sedorovitz M / Flohr K / Campello L / Hartung JE / Hogle B / Gillespie M / Schriever H / Aweidah H / Koester J / Clausen I / Seeber S / Revelant F / Schreurs R / Koechl F / Sieving PA / Sahel JA / Stauffer WR / Peixoto RT / Fauser S / Lin R / Conway J / Da Silva S / Krol J / Betegon M / Byrne LC
History
DepositionNov 24, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74043.png

Downloads & links

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Map

FileDownload / File: emd_74043.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of the engineered vector AAV2.ATX002
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 512 pix.
= 368.64 Å		0.72 Å/pix.
x 512 pix.
= 368.64 Å		0.72 Å/pix.
x 512 pix.
= 368.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.028540151 - 0.03957471
Average (Standard dev.)0.000015277752 (±0.0025988643)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 368.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_74043_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_74043_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_74043_half_map_2.map
AnnotationHalf Map A
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: Engineered AAV2 capsid protein VP3

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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

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Macromolecule #1: Engineered AAV2 capsid protein VP3

MacromoleculeName: Engineered AAV2 capsid protein VP3 / type: protein_or_peptide / ID: 1
Details: Engineered AAV2 capsid VP3 protein with a 9AA insertion.
Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: adeno-associated virus 2
Molecular weightTheoretical: 61.140199 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATGSGAPMA DNNEGADGVG NSSGNWHCDS TWMGDRVITT STRTWALPTY NNHLYKQISS QSGASNDNHY FGYSTPWGYF DFNRFHCHF SPRDWQRLIN NNWGFRPKRL NFKLFNIQVK EVTQNDGTTT IANNLTSTVQ VFTDSEYQLP YVLGSAHQGC L PPFPADVF ...String:
MATGSGAPMA DNNEGADGVG NSSGNWHCDS TWMGDRVITT STRTWALPTY NNHLYKQISS QSGASNDNHY FGYSTPWGYF DFNRFHCHF SPRDWQRLIN NNWGFRPKRL NFKLFNIQVK EVTQNDGTTT IANNLTSTVQ VFTDSEYQLP YVLGSAHQGC L PPFPADVF MVPQYGYLTL NNGSQAVGRS SFYCLEYFPS QMLRTGNNFT FSYTFEDVPF HSSYAHSQSL DRLMNPLIDQ YL YYLSRTN TPSGTTTQSR LQFSQAGASD IRDQSRNWLP GPCYRQQRVS KTSADNNNSE YSWTGATKYH LNGRDSLVNP GPA MASHKD DEEKFFPQSG VLIFGKQGSE KTNVDIEKVM ITDEEEIRTT NPVATEQYGS VSTNLQRGNL AEHQTRPARQ AATA DVNTQ GVLPGMVWQD RDVYLQGPIW AKIPHTDGHF HPSPLMGGFG LKHPPPQILI KNTPVPANPS TTFSAAKFAS FITQY STGQ VSVEIEWELQ KENSKRWNPE IQYTSNYNKS INVDFTVDTN GVYSEPRPIG TRYLTRNL

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 / Details: DPBS
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 10377 / Average exposure time: 2.43 sec. / Average electron dose: 30.0 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 / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 160533
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Details: Ewald sphere correction applied in RELION 5.0 / Number images used: 14969
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final 3D classificationNumber classes: 62 / Avg.num./class: 500 / Software - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6u0r


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation
Output model

PDB-9zcw:
Cryo-EM structure of the engineered vector AAV2.ATX002

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Atomic model buiding 2

Initial modelChain - Source name: Other / Chain - Initial model type: other / Details: ModelAngelo
DetailsAb initio model created with ModelAngelo
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9zcw:
Cryo-EM structure of the engineered vector AAV2.ATX002

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