+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9797 | |||||||||
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Title | AAV5 in neutral condition at 3.18 Ang | |||||||||
Map data | ||||||||||
Sample |
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Keywords | adeno-associated virus / AAV5 / 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 - 5 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.18 Å | |||||||||
Authors | Lou Z / Zhang R | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2019 Title: Divergent engagements between adeno-associated viruses with their cellular receptor AAVR. Authors: Ran Zhang / Guangxue Xu / Lin Cao / Zixian Sun / Yong He / Mengtian Cui / Yuna Sun / Shentao Li / Huapeng Li / Lan Qin / Mingxu Hu / Zhengjia Yuan / Zipei Rao / Wei Ding / Zihe Rao / Zhiyong Lou / Abstract: Adeno-associated virus (AAV) receptor (AAVR) is an essential receptor for the entry of multiple AAV serotypes with divergent rules; however, the mechanism remains unclear. Here, we determine the ...Adeno-associated virus (AAV) receptor (AAVR) is an essential receptor for the entry of multiple AAV serotypes with divergent rules; however, the mechanism remains unclear. Here, we determine the structures of the AAV1-AAVR and AAV5-AAVR complexes, revealing the molecular details by which PKD1 recognizes AAV5 and PKD2 is solely engaged with AAV1. PKD2 lies on the plateau region of the AAV1 capsid. However, the AAV5-AAVR interface is strikingly different, in which PKD1 is bound at the opposite side of the spike of the AAV5 capsid than the PKD2-interacting region of AAV1. Residues in strands F/G and the CD loop of PKD1 interact directly with AAV5, whereas residues in strands B/C/E and the BC loop of PKD2 make contact with AAV1. These findings further the understanding of the distinct mechanisms by which AAVR recognizes various AAV serotypes and provide an example of a single receptor engaging multiple viral serotypes with divergent rules. | |||||||||
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_9797.map.gz | 54 MB | EMDB map data format | |
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Header (meta data) | emd-9797-v30.xml emd-9797.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
Images | emd_9797.png | 209.6 KB | ||
Filedesc metadata | emd-9797.cif.gz | 5.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9797 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9797 | HTTPS FTP |
-Validation report
Summary document | emd_9797_validation.pdf.gz | 646 KB | Display | EMDB validaton report |
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Full document | emd_9797_full_validation.pdf.gz | 645.6 KB | Display | |
Data in XML | emd_9797_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | emd_9797_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9797 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9797 | HTTPS FTP |
-Related structure data
Related structure data | 6jctMC 9794C 9795C 9796C 6jcqC 6jcrC 6jcsC 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_9797.map.gz / Format: CCP4 / Size: 209.3 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: 0.93 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 - 5
Entire | Name: Adeno-associated virus - 5 |
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Components |
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-Supramolecule #1: Adeno-associated virus - 5
Supramolecule | Name: 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: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: homo sapiens (human) |
-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Adeno-associated virus - 5 |
Molecular weight | Theoretical: 58.213078 KDa |
Sequence | String: DGVGNASGDW HCDSTWMGDR VVTKSTRTWV LPSYNNHQYR EIKSGSVDGS NANAYFGYST PWGYFDFNRF HSHWSPRDWQ RLINNYWGF RPRSLRVKIF NIQVKEVTVQ DSTTTIANNL TSTVQVFTDD DYQLPYVVGN GTEGCLPAFP PQVFTLPQYG Y ATLNRDNT ...String: DGVGNASGDW HCDSTWMGDR VVTKSTRTWV LPSYNNHQYR EIKSGSVDGS NANAYFGYST PWGYFDFNRF HSHWSPRDWQ RLINNYWGF RPRSLRVKIF NIQVKEVTVQ DSTTTIANNL TSTVQVFTDD DYQLPYVVGN GTEGCLPAFP PQVFTLPQYG Y ATLNRDNT ENPTERSSFF CLEYFPSKML RTGNNFEFTY NFEEVPFHSS FAPSQNLFKL ANPLVDQYLY RFVSTNNTGG VQ FNKNLAG RYANTYKNWF PGPMGRTQGW NLGSGVNRAS VSAFATTNRM ELEGASYQVP PQPNGMTNNL QGSNTYALEN TMI FNSQPA NPGTTATYLE GNMLITSESE TQPVNRVAYN VGGQMATNNQ SSTTAPATGT YNLQEIVPGS VWMERDVYLQ GPIW AKIPE TGAHFHPSPA MGGFGLKHPP PMMLIKNTPV PGNITSFSDV PVSSFITQYS TGQVTVEMEW ELKKENSKRW NPEIQ YTNN YNDPQFVDFA PDSTGEYRTT RPIGTRYLTR PL UniProtKB: Capsid protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | 2D array |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 1.6 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2900 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |