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- EMDB-23516: Hum8 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-23516
TitleHum8 capsid
Map data
Sample
  • Virus: Adeno-associated virus
    • Protein or peptide: Capsid protein
  • Ligand: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
KeywordsIcosahedral Capsid / AAV8 / Hum8 / capsid engineering / Adeno-associated virus / Parvovirus / Gene Therapy / VIRUS
Function / homology
Function and homology information


T=1 icosahedral viral capsid / nucleotide binding / 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 - 8 / Adeno-associated virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.49 Å
AuthorsMietzsch M / Agbandje-McKenna M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
CitationJournal: J Virol / Year: 2021
Title: Receptor Switching in Newly Evolved Adeno-associated Viruses.
Authors: L Patrick Havlik / Anshuman Das / Mario Mietzsch / Daniel K Oh / Jonathan Ark / Robert McKenna / Mavis Agbandje-McKenna / Aravind Asokan /
Abstract: Adeno-associated viruses utilize different glycans and the AAV receptor (AAVR) for cellular attachment and entry. Directed evolution has yielded new AAV variants; however, structure-function ...Adeno-associated viruses utilize different glycans and the AAV receptor (AAVR) for cellular attachment and entry. Directed evolution has yielded new AAV variants; however, structure-function correlates underlying their improved transduction are generally overlooked. Here, we report that infectious cycling of structurally diverse AAV surface loop libraries yields functionally distinct variants. Newly evolved variants show enhanced cellular binding, uptake, and transduction, but through distinct mechanisms. Using glycan-based and genome-wide CRISPR knockout screens, we discover that one AAV variant acquires the ability to recognize sulfated glycosaminoglycans, while another displays receptor switching from AAVR to integrin β1 (ITGB1). A previously evolved variant, AAVhum.8, preferentially utilizes the ITGB1 receptor over AAVR. Visualization of the AAVhum.8 capsid by cryoelectron microscopy at 2.49-Å resolution localizes the newly acquired integrin recognition motif adjacent to the AAVR footprint. These observations underscore the new finding that distinct AAV surface epitopes can be evolved to exploit different cellular receptors for enhanced transduction. Understanding how viruses interact with host cells through cell surface receptors is central to discovery and development of antiviral therapeutics, vaccines, and gene transfer vectors. Here, we demonstrate that distinct epitopes on the surface of adeno-associated viruses can be evolved by infectious cycling to recognize different cell surface carbohydrates and glycoprotein receptors and solve the three-dimensional structure of one such newly evolved AAV capsid, which provides a roadmap for designing viruses with improved attributes for gene therapy applications.
History
DepositionFeb 19, 2021-
Header (metadata) releaseJul 7, 2021-
Map releaseJul 7, 2021-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ltm
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ltm
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23516.png

Downloads & links

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Map

FileDownload / File: emd_23516.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.1 Å/pix.
x 420 pix.
= 460.32 Å		1.1 Å/pix.
x 420 pix.
= 460.32 Å		1.1 Å/pix.
x 420 pix.
= 460.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.096 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5 / Movie #1: 3
Minimum - Maximum-10.276827000000001 - 18.198957
Average (Standard dev.)0.000000002410546 (±1.0000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-210-210-210
Dimensions420420420
Spacing420420420
CellA=B=C: 460.31998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0961.0961.096
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z460.320460.320460.320
α/β/γ90.00090.00090.000
start NX/NY/NZ-210-210-210
NX/NY/NZ420420420
MAP C/R/S213
start NC/NR/NS-210-210-210
NC/NR/NS420420420
D min/max/mean-10.27718.1990.000

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Supplemental data

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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
  • Ligand: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE

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Supramolecule #1: Adeno-associated virus

SupramoleculeName: Adeno-associated virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 272636 / Sci species name: Adeno-associated virus / Sci species strain: Hum8 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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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 - 8
Molecular weightTheoretical: 58.491398 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DGVGSSSGNW HCDSTWLGDR VITTSTRTWA LPTYNNHLYK QISNGTSGGA TNDNTYFGYS TPWGYFDFNR FHCHFSPRDW QRLINNNWG FRPKRLSFKL FNIQVKEVTQ NEGTKTIANN LTSTIQVFTD SEYQLPYVLG SAHQGCLPPF PADVFMIPQY G YLTLNNGS ...String:
DGVGSSSGNW HCDSTWLGDR VITTSTRTWA LPTYNNHLYK QISNGTSGGA TNDNTYFGYS TPWGYFDFNR FHCHFSPRDW QRLINNNWG FRPKRLSFKL FNIQVKEVTQ NEGTKTIANN LTSTIQVFTD SEYQLPYVLG SAHQGCLPPF PADVFMIPQY G YLTLNNGS QAVGRSSFYC LEYFPSQMLR TGNNFQFTYT FEDVPFHSSY AHSQSLDRLM NPLIDQYLYY LSRTQTTSNG RG VTLGFSQ GGPNTMANQA KNWLPGPCYR QQRVSTYPLQ NNNSNFAWTA GTKYHLNGRN SLANPGIAMA THKDDEERFF PSN GILIFG KQNAARDNAD YSDVMLTSEE EIKTTNPVAT EEYGIVADNG QTQTTAPQIG TVNSQGALPG MVWQNRDVYL QGPI WAKIP HTDGNFHPSP LMGGFGLKHP PPQILIKNTP VPADPRSTFN GDKLNSFITQ YSTGQVSVEI EWELQKENSK RWNPE IQYT SNYYKSTSVD FAVNTEGVYS EPRPIGTRYL TRNL

UniProtKB: Capsid protein

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Macromolecule #2: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE

MacromoleculeName: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / type: ligand / ID: 2 / Number of copies: 60 / Formula: D5M
Molecular weightTheoretical: 331.222 Da
Chemical component information

ChemComp-D5M:
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE

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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: GATAN K3 (6k x 4k) / Average electron dose: 60.0 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

CTF correctionSoftware - Name: cisTEM / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 275883
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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