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Yorodumi- EMDB-25910: Adeno-associated virus Go.1 in Complex With Its Cellular Receptor... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25910 | |||||||||
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Title | Adeno-associated virus Go.1 in Complex With Its Cellular Receptor AAVR at 2.4 Angstroms Resolution, AAVGo.1 AAVR | |||||||||
Map data | Cryo-EM map of AAV-Go.1 bound to the PKD1 subunit of its receptor, AAVR. Pixel size of 0.661 Angstroms. | |||||||||
Sample |
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Keywords | AAVGo.1 / AAV / AAV-Go / AAVR / adeno-associated virus / PKD domain / parvovirus / gene therapy / receptor / adeno-associated virus receptor / PKD1 / PKD / VIRUS LIKE PARTICLE | |||||||||
Function / homology | Function and homology information T=1 icosahedral viral capsid / neuron migration / cytoplasmic vesicle / Golgi membrane / nucleolus / structural molecule activity / Golgi apparatus / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Adeno-associated virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.4 Å | |||||||||
Authors | Silveria M / Large E | |||||||||
Funding support | United States, 1 items
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Citation | Journal: J Virol / Year: 2022 Title: Cross-Species Permissivity: Structure of a Goat Adeno-Associated Virus and Its Complex with the Human Receptor AAVR. Authors: Edward E Large / Mark A Silveria / Onellah Weerakoon / Tommi A White / Michael S Chapman / Abstract: Adeno-associated virus (AAV) is a small ssDNA satellite virus of high interest (in recombinant form) as a safe and effective gene therapy vector. AAV's human cell entry receptor (AAVR) contains ...Adeno-associated virus (AAV) is a small ssDNA satellite virus of high interest (in recombinant form) as a safe and effective gene therapy vector. AAV's human cell entry receptor (AAVR) contains polycystic kidney disease (PKD) domains bound by AAV. Seeking understanding of the spectrum of interactions, goat AAVGo.1 is investigated, because its host is the species most distant from human with reciprocal cross-species cell susceptibility. The structure of AAVGo.1, solved by cryo-EM to 2.9 Å resolution, is most similar to AAV5. Through ELISA (enzyme-linked immunosorbent assay) studies, it is shown that AAVGo.1 binds to human AAVR more strongly than do AAV2 or AAV5, and that it joins AAV5 in a class that binds exclusively to PKD domain 1 (PKD1), in contrast to other AAVs that interact primarily with PKD2. The AAVGo.1 cryo-EM structure of a complex with a PKD12 fragment of AAVR at 2.4 Å resolution shows PKD1 bound with minimal change in virus structure. There are only minor conformational adaptations in AAVR, but there is a near-rigid rotation of PKD1 with maximal displacement of the receptor domain by ~1 Å compared to PKD1 bound to AAV5. AAVGo.1 joins AAV5 as the second member of an emerging class of AAVs whose mode of receptor-binding is completely different from other AAVs, typified by AAV2. Adeno-associated virus (AAV) is a small ssDNA satellite parvovirus. As a recombinant vector with a protein shell encapsidating a transgene, recombinant AAV (rAAV) is a leading delivery vehicle for gene therapy, with two FDA-approved treatments and 150 clinical trials for 30 diseases. The human entry receptor AAVR has five PKD domains. To date, all serotypes, except AAV5, have interacted primarily with the second PKD domain, PKD2. Goat is the AAV host most distant from human with cross-species cell infectivity. AAVGo.1 is similar in structure to AAV5, the two forming a class with a distinct mode of receptor-binding. Within the two classes, binding interactions are mostly conserved, giving an indication of the latitude available in modulating delivery vectors. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25910.map.gz | 531.2 MB | EMDB map data format | |
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Header (meta data) | emd-25910-v30.xml emd-25910.xml | 16.8 KB 16.8 KB | Display Display | EMDB header |
Images | emd_25910.png | 77.7 KB | ||
Filedesc metadata | emd-25910.cif.gz | 7.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25910 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25910 | HTTPS FTP |
-Validation report
Summary document | emd_25910_validation.pdf.gz | 818.1 KB | Display | EMDB validaton report |
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Full document | emd_25910_full_validation.pdf.gz | 817.7 KB | Display | |
Data in XML | emd_25910_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | emd_25910_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25910 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25910 | HTTPS FTP |
-Related structure data
Related structure data | 7ti5MC 7ti4C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_25910.map.gz / Format: CCP4 / Size: 567.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of AAV-Go.1 bound to the PKD1 subunit of its receptor, AAVR. Pixel size of 0.661 Angstroms. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.66109 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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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: all Details: Expressed using SF9 cells with a pfastbac LIC vector. Purified with cesium chloride ultracentrifugation. NCBI-ID: 272636 / Sci species name: Adeno-associated virus / Sci species strain: AAV Go.1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 3.746 MDa |
Virus shell | Shell ID: 1 / Name: Capsid, VP3 / Diameter: 250.0 Å / T number (triangulation number): 1 |
-Macromolecule #1: Dyslexia-associated protein KIAA0319-like protein
Macromolecule | Name: Dyslexia-associated protein KIAA0319-like protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 31.837385 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MASVSAGESV QITLPKNEVQ LNAYVLQEPP KGETYTYDWQ LITHPRDYSG EMEGKHSQIL KLSKLTPGLY EFKVIVEGQN AHGEGYVNV TVKPEPRKNR PPIAIVSPQF QEISLPTTST VIDGSQSTDD DKIVQYHWEE LKGPLREEKI SEDTAILKLS K LVPGNYTF ...String: MASVSAGESV QITLPKNEVQ LNAYVLQEPP KGETYTYDWQ LITHPRDYSG EMEGKHSQIL KLSKLTPGLY EFKVIVEGQN AHGEGYVNV TVKPEPRKNR PPIAIVSPQF QEISLPTTST VIDGSQSTDD DKIVQYHWEE LKGPLREEKI SEDTAILKLS K LVPGNYTF SLTVVDSDGA TNSTTANLTV NKAVDYPPVA NAGPNQVITL PQNSITLFGN QSTDDHGITS YEWSLSPSSK GK VVEMQGV RTPTLQLSAM QEGDYTYQLT VTDTIGQQAT AQVTVIVQPE NNK UniProtKB: Dyslexia-associated protein KIAA0319-like protein |
-Macromolecule #2: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Adeno-associated virus |
Molecular weight | Theoretical: 80.691594 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MSFVDHPPDW LEEVGEGLRE FLGLEAGPPK PKPNQQHQDQ ARGLVLPGYN YLGPGNGLDR GEPVNRADEV AREHDISYNE QLEAGDNPY LKYNHADAEF QEKLADDTSF GGNLGKAVFQ AKKRVLEPFG LVEEGAKTAP TGKRIDDHFP KRKKARTEED S KPSTSSDA ...String: MSFVDHPPDW LEEVGEGLRE FLGLEAGPPK PKPNQQHQDQ ARGLVLPGYN YLGPGNGLDR GEPVNRADEV AREHDISYNE QLEAGDNPY LKYNHADAEF QEKLADDTSF GGNLGKAVFQ AKKRVLEPFG LVEEGAKTAP TGKRIDDHFP KRKKARTEED S KPSTSSDA EAGPSGSQQL QIPAQPASSL GADTMSAGGG GPLGDNNQGA DGVGNASGDW HCDSTWMGDR VVTKSTRTWV LP SYNNHQY REIKSGSVDG SNANAYFGYS TPWGYFDFNR FHSHWSPRDW QRLINNYWGF RPRSLRVKIF NIQVKEVTVQ DST TTIANN LTSTVQVFTD DDYQLPYVVG NGTEGCLPAF PPQVFTLPQY GYATLNRDNG DNPTERSSFF CLEYFPSKML RTGN NFEFT YSFEEVPFHC SFAPSQNLFK LANPLVDQYL YRFVSTSATG AIQFQKNLAG RYANTYKNWF PGPMGRTQGW NTSSG SSTN RVSVNNFSVS NRMNLEGASY QVNPQPNGMT NTLQGSNRYA LENTMIFNAQ NATPGTTSVY PEDNLLLTSE SETQPV NRV AYNTGGQMAT NAQNATTAPT VGTYNLQEVL PGSVWMERDV YLQGPIWAKI PETGAHFHPS PAMGGFGLKH PPPMMLI KN TPVPGNITSF SDVPVSSFIT QYSTGQVTVE MEWELKKENS KRWNPEIQYT NNYNDPQFVD FAPDGSGEYR TTRAIGTR Y LTRPL UniProtKB: Capsid protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.75 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K Details: Two 2uL aliquots applied to grid (manual blotting between), prior to automated 3 second blot before plunging.. | ||||||||||||
Details | Monodisperse |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 93.0 K / Max: 93.0 K |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Average electron dose: 32.9 e/Å2 / Details: Pixel size was 0.664 angstrom. |
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 / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 6400 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Details | Stand-alone RSRef was used for refinement of magnification, resolution, envelope correction and atomic B-factors. This was alternated with RSRef-embedded CNS was used for molecular dynamics optimization (1st round) and stereochemically-restrained all-atom least-squares optimization. | ||||||
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Least-squares residual | ||||||
Output model | PDB-7ti5: |