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- EMDB-65077: Adeno-Associated Virus 6-M2, AAV6-M2 -

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Basic information

Entry
Database: EMDB / ID: EMD-65077
TitleAdeno-Associated Virus 6-M2, AAV6-M2
Map data
Sample
  • Virus: Adeno-associated virus
    • Protein or peptide: Capsid protein VP1
KeywordsAdeno-Associated Virus / AAV6 variant / VIRUS
Function / homologyPhospholipase 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 / T=1 icosahedral viral capsid / structural molecule activity / Capsid protein VP1
Function and homology information
Biological speciesAdeno-associated virus
Methodsingle particle reconstruction / cryo EM / Resolution: 1.8 Å
AuthorsZheng R / Ma L
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Vita / Year: 2026
Title: An AAV variant enables human T cell engineering in vivo
Authors: Lu Z / Ni K / Liu W / Song Q / Zheng R / Wei M / Zhang Y / Wang J / Wei L / Wu C / Zhang Q / Wu J / Ding S / Zhu R / Cheng C / Cong Y / Xu Y / Kong B / Wu S / Wang G / Wang X / Wang Y / Qian ...Authors: Lu Z / Ni K / Liu W / Song Q / Zheng R / Wei M / Zhang Y / Wang J / Wei L / Wu C / Zhang Q / Wu J / Ding S / Zhu R / Cheng C / Cong Y / Xu Y / Kong B / Wu S / Wang G / Wang X / Wang Y / Qian X / Deng R / Chen H / Li Y / Ma L
History
DepositionJun 17, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65077.png

Downloads & links

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Map

FileDownload / File: emd_65077.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 640 pix.
= 420.672 Å		0.66 Å/pix.
x 640 pix.
= 420.672 Å		0.66 Å/pix.
x 640 pix.
= 420.672 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6573 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.2670968 - 2.8806353
Average (Standard dev.)0.0035268157 (±0.110857494)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 420.672 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65077_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65077_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65077_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

EntireName: Adeno-associated virus
Components
  • Virus: Adeno-associated virus
    • Protein or peptide: Capsid protein VP1

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Supramolecule #1: Adeno-associated virus

SupramoleculeName: Adeno-associated virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 272636 / Sci species name: Adeno-associated virus / 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: 1 / Enantiomer: LEVO
Source (natural)Organism: Adeno-associated virus
Molecular weightTheoretical: 58.292492 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VGNASGNWHC DSTWLGDRVI TTSTRTWALP TYNNHLYKQI SSASTGASND NHYFGYSTPW GYFDFNRFHC HFSPRDWQRL INNNWGFRP KRLNFKLFNI QVKEVTTNDG VTTIANNLTS TVQVFSDSEY QLPYVLGSAH QGCLPPFPAD VFMIPQYGYL T LNNGSQAV ...String:
VGNASGNWHC DSTWLGDRVI TTSTRTWALP TYNNHLYKQI SSASTGASND NHYFGYSTPW GYFDFNRFHC HFSPRDWQRL INNNWGFRP KRLNFKLFNI QVKEVTTNDG VTTIANNLTS TVQVFSDSEY QLPYVLGSAH QGCLPPFPAD VFMIPQYGYL T LNNGSQAV GRSSFYCLEY FPSQMLRTGN NFTFSYTFED VPFHSSYAHS QSLDRLMNPL IDQYLYYLNR TQNQSGSAQN KD LLFSRGS PAGMSVQPKN WLPGPCYRQQ RVSKTKTDNN NSNFTWTGAS KYNLNGRESI INPGTAMASH KDDKDKFFPM SGV MIFGKE SAGASNTALD NVMITDEEEI KATNPVATER FGTVATNHQS VNYEEETGDV HVMGALPGMV WQDRDVYLQG PIWA KIPHT DGHFHPSPLM GGFGLKHPPP QILIKNTPVP ANPPAEFSAT KFASFITQYS TGQVSVEIEW ELQKENSKRW NPEVQ YTSN YAKSANVDFT VDNNGLYTEP RPIGTRYLTR PL

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: 7.23
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 156281
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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