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- EMDB-46745: AAV5 at 80 Degree Celsius -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-46745
TitleAAV5 at 80 Degree Celsius
Map data
Sample
  • Virus: adeno-associated virus 5
    • Protein or peptide: Capsid protein
KeywordsTemperature / Virus / Adeno-Associated Virus / Genome
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 5
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsMcKenna R / Bennett A / Gliwa K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
CitationJournal: to be published
Title: Biophysical and Structural Insights into AAV Genome Ejection
Authors: McKenna R / Bennett A / Gliwa K
History
DepositionAug 25, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46745.png

Downloads & links

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Map

FileDownload / File: emd_46745.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 500 pix.
= 467.5 Å		0.94 Å/pix.
x 500 pix.
= 467.5 Å		0.94 Å/pix.
x 500 pix.
= 467.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.935 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 2.0
Minimum - Maximum-13.993296000000001 - 22.046692
Average (Standard dev.)0.000000000858888 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-250-250-250
Dimensions500500500
Spacing500500500
CellA=B=C: 467.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_46745_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_46745_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : adeno-associated virus 5

EntireName: adeno-associated virus 5
Components
  • Virus: adeno-associated virus 5
    • Protein or peptide: Capsid protein

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Supramolecule #1: adeno-associated virus 5

SupramoleculeName: adeno-associated virus 5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 82300 / Sci species name: adeno-associated virus 5 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No
Molecular weightTheoretical: 4 MDa
Virus shellShell ID: 1 / Diameter: 260.0 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: 60 / Enantiomer: LEVO
Source (natural)Organism: adeno-associated virus 5
Molecular weightTheoretical: 80.497414 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSFVDHPPDW LEEVGEGLRE FLGLEAGPPK PKPNQQHQDQ ARGLVLPGYN YLGPGNGLDR GEPVNRADEV AREHDISYNE QLEAGDNPY LKYNHADAEF QEKLADDTSF GGNLGKAVFQ AKKRVLEPFG LVEEGAKTAP TGKRIDDHFP KRKKARTEED S KPSTSSDA ...String:
MSFVDHPPDW LEEVGEGLRE FLGLEAGPPK PKPNQQHQDQ ARGLVLPGYN YLGPGNGLDR GEPVNRADEV AREHDISYNE QLEAGDNPY LKYNHADAEF QEKLADDTSF GGNLGKAVFQ AKKRVLEPFG LVEEGAKTAP TGKRIDDHFP KRKKARTEED S KPSTSSDA EAGPSGSQQL QIPAQPASSL GADTMSAGGG GPLGDNNQGA DGVGNASGDW HCDSTWMGDR VVTKSTRTWV LP SYNNHQY REIKSGSVDG SNANAYFGYS TPWGYFDFNR FHSHWSPRDW QRLINNYWGF RPRSLRVKIF NIQVKEVTVQ DST TTIANN LTSTVQVFTD DDYQLPYVVG NGTEGCLPAF PPQVFTLPQY GYATLNRDNT ENPTERSSFF CLEYFPSKML RTGN NFEFT YNFEEVPFHS SFAPSQNLFK LANPLVDQYL YRFVSTNNTG GVQFNKNLAG RYANTYKNWF PGPMGRTQGW NLGSG VNRA SVSAFATTNR MELEGASYQV PPQPNGMTNN LQGSNTYALE NTMIFNSQPA NPGTTATYLE GNMLITSESE TQPVNR VAY NVGGQMATNN QSSTTAPATG TYNLQEIVPG SVWMERDVYL QGPIWAKIPE TGAHFHPSPA MGGFGLKHPP PMMLIKN TP VPGNITSFSD VPVSSFITQY STGQVTVEME WELKKENSKR WNPEIQYTNN YNDPQFVDFA PDSTGEYRTT RPIGTRYL T RPL

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

Concentration0.5 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DARK FIELD / Nominal defocus max: 3.8000000000000003 µm / Nominal defocus min: 1.26 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 44589
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3ntt

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44589
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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