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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Cryo-EM Structure of AAV2-R404A Variant | |||||||||
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![]() | Symmetry / capsid / AAV2 / VIRUS | |||||||||
Function / homology | ![]() permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell nucleolus / T=1 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / structural molecule activity Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.62 Å | |||||||||
![]() | Bennett AD / McKenna R | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM Structure of genome containing AAV2 Authors: Bennett AD / Mckenna R | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 226.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.9 KB 14.9 KB | Display Display | ![]() |
Images | ![]() | 125.6 KB | ||
Filedesc metadata | ![]() | 5.8 KB | ||
Others | ![]() ![]() | 60.8 MB 60.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1008.4 KB | Display | ![]() |
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Full document | ![]() | 1007.9 KB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 19.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8fznMC ![]() 8fywC ![]() 8fz0C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.962 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_29636_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_29636_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : adeno-associated virus 2
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: adeno-associated virus 2
Supramolecule | Name: adeno-associated virus 2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10804 / Sci species name: adeno-associated virus 2 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() |
Molecular weight | Theoretical: 3.9 MDa |
Virus shell | Shell ID: 1 / Name: capsid / Diameter: 26.0 Å / T number (triangulation number): 1 |
-Macromolecule #1: Capsid protein VP1
Macromolecule | Name: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 56.722445 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GDRVITTSTR TWALPTYNNH LYKQISSQSG ASNDNHYFGY STPWGYFDFN RFHCHFSPRD WQRLINNNWG FRPKRLNFKL FNIQVKEVT QNDGTTTIAN NLTSTVQVFT DSEYQLPYVL GSAHQGCLPP FPADVFMVPQ YGYLTLNNGS QAVGRSSFYC L EYFPSQML ...String: GDRVITTSTR TWALPTYNNH LYKQISSQSG ASNDNHYFGY STPWGYFDFN RFHCHFSPRD WQRLINNNWG FRPKRLNFKL FNIQVKEVT QNDGTTTIAN NLTSTVQVFT DSEYQLPYVL GSAHQGCLPP FPADVFMVPQ YGYLTLNNGS QAVGRSSFYC L EYFPSQML ATGNNFTFSY TFEDVPFHSS YAHSQSLDRL MNPLIDQYLY YLSRTNTPSG TTTQSRLQFS QAGASDIRDQ SR NWLPGPC YRQQRVSKTS ADNNNSEYSW TGATKYHLNG RDSLVNPGPA MASHKDDEEK FFPQSGVLIF GKQGSEKTNV DIE KVMITD EEEIRTTNPV ATEQYGSVST NLQRGNRQAA TADVNTQGVL PGMVWQDRDV YLQGPIWAKI PHTDGHFHPS PLMG GFGLK HPPPQILIKN TPVPANPSTT FSAAKFASFI TQYSTGQVSV EIEWELQKEN SKRWNPEIQY TSNYNKSVNV DFTVD TNGV YSEPRPIGTR YLTRNL UniProtKB: Capsid protein VP1 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.3 / Component - Concentration: 1.0 mM / Component - Formula: PBS-MK / Component - Name: TD / Details: 1XPBS, 1 mM MgCl2, 2.5 mM KCl pH7.3 |
Grid | Model: Quantifoil / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Number real images: 1674 / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 23783 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-8fzn: |