+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23516 | |||||||||
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Title | Hum8 capsid | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Icosahedral Capsid / AAV8 / Hum8 / capsid engineering / Adeno-associated virus / Parvovirus / Gene Therapy / VIRUS | |||||||||
Function / homology | 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 / T=1 icosahedral viral capsid / structural molecule activity / Capsid protein Function and homology information | |||||||||
Biological species | Adeno-associated virus - 8 / Adeno-associated virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.49 Å | |||||||||
Authors | Mietzsch M / Agbandje-McKenna M | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23516.map.gz | 262.8 MB | EMDB map data format | |
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Header (meta data) | emd-23516-v30.xml emd-23516.xml | 10.1 KB 10.1 KB | Display Display | EMDB header |
Images | emd_23516.png | 323.2 KB | ||
Filedesc metadata | emd-23516.cif.gz | 5.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23516 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23516 | HTTPS FTP |
-Validation report
Summary document | emd_23516_validation.pdf.gz | 740.3 KB | Display | EMDB validaton report |
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Full document | emd_23516_full_validation.pdf.gz | 739.9 KB | Display | |
Data in XML | emd_23516_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | emd_23516_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23516 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23516 | HTTPS FTP |
-Related structure data
Related structure data | 7ltmMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23516.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.096 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Adeno-associated virus
Entire | Name: Adeno-associated virus |
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Components |
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-Supramolecule #1: Adeno-associated virus
Supramolecule | Name: 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
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO |
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Source (natural) | Organism: Adeno-associated virus - 8 |
Molecular weight | Theoretical: 58.491398 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
Macromolecule | Name: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / type: ligand / ID: 2 / Number of copies: 60 / Formula: D5M |
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Molecular weight | Theoretical: 331.222 Da |
Chemical component information | ChemComp-D5M: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 275883 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: RANDOM ASSIGNMENT |