+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36311 | ||||||||||||
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Title | Cryo-EM Structure of 3-axis block of AAV9P31-Car4 complex | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | receptor / aav9p31 / Carbonic anhydrases iv / Block-based reconstruction / VIRUS / VIRAL PROTEIN-LYASE complex | ||||||||||||
Function / homology | Function and homology information Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Reversible hydration of carbon dioxide / regulation of pH / bicarbonate transport / T=1 icosahedral viral capsid / transport vesicle membrane / endoplasmic reticulum-Golgi intermediate compartment / rough endoplasmic reticulum / secretory granule membrane ...Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Reversible hydration of carbon dioxide / regulation of pH / bicarbonate transport / T=1 icosahedral viral capsid / transport vesicle membrane / endoplasmic reticulum-Golgi intermediate compartment / rough endoplasmic reticulum / secretory granule membrane / sarcoplasmic reticulum / carbonic anhydrase / brush border membrane / carbonate dehydratase activity / carbon dioxide transport / trans-Golgi network / sarcolemma / one-carbon metabolic process / apical plasma membrane / external side of plasma membrane / structural molecule activity / perinuclear region of cytoplasm / zinc ion binding / extracellular exosome / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) / Adeno-associated virus 9 | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.28 Å | ||||||||||||
Authors | Zhang R / Liu Y / Lou Z | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: PLoS Pathog / Year: 2024 Title: Structural basis of the recognition of adeno-associated virus by the neurological system-related receptor carbonic anhydrase IV. Authors: Ran Zhang / Yixiao Liu / Fengxi Yu / Guangxue Xu / Lili Li / Baobin Li / Zhiyong Lou / Abstract: Carbonic anhydrase IV (Car4) is a newly identified receptor that allows adeno-associated virus (AAV) 9P31 to cross the blood-brain barrier and achieve efficient infection in the central nervous ...Carbonic anhydrase IV (Car4) is a newly identified receptor that allows adeno-associated virus (AAV) 9P31 to cross the blood-brain barrier and achieve efficient infection in the central nervous system (CNS) in mouse models. However, the molecular mechanism by which engineered AAV capsids with 7-mer insertion in the variable region (VR) VIII recognize these novel cellular receptors is unknown. Here we report the cryo-EM structures of AAV9P31 and its complex with Mus musculus Car4 at atomic resolution by utilizing the block-based reconstruction (BBR) method. The structures demonstrated that Car4 binds to the protrusions at 3-fold axes of the capsid. The inserted 7-mer extends into a hydrophobic region near the catalytic center of Car4 to form stable interactions. Mutagenesis studies also identified the key residues in Car4 responsible for the AAV9P31 interaction. These findings provide new insights into the novel receptor recognition mechanism of AAV generated by directed evolution and highlight the application of the BBR method to studying the virus-receptor molecular mechanism. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36311.map.gz | 14.1 MB | EMDB map data format | |
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Header (meta data) | emd-36311-v30.xml emd-36311.xml | 18 KB 18 KB | Display Display | EMDB header |
Images | emd_36311.png | 43 KB | ||
Filedesc metadata | emd-36311.cif.gz | 6.3 KB | ||
Others | emd_36311_half_map_1.map.gz emd_36311_half_map_2.map.gz | 11.8 MB 11.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36311 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36311 | HTTPS FTP |
-Validation report
Summary document | emd_36311_validation.pdf.gz | 840 KB | Display | EMDB validaton report |
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Full document | emd_36311_full_validation.pdf.gz | 839.6 KB | Display | |
Data in XML | emd_36311_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | emd_36311_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36311 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36311 | HTTPS FTP |
-Related structure data
Related structure data | 8jifMC 8xegC 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_36311.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.8433 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_36311_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36311_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 3-fold axes block of AAV9P31 and Car4 complex aat 2.28 angstrom
Entire | Name: 3-fold axes block of AAV9P31 and Car4 complex aat 2.28 angstrom |
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Components |
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-Supramolecule #1: 3-fold axes block of AAV9P31 and Car4 complex aat 2.28 angstrom
Supramolecule | Name: 3-fold axes block of AAV9P31 and Car4 complex aat 2.28 angstrom type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Macromolecule #1: Carbonic anhydrase 4
Macromolecule | Name: Carbonic anhydrase 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: carbonic anhydrase |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 29.281367 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: WCYEIQTKDP RSSCLGPEKW PGACKENQQS PINIVTARTK VNPRLTPFIL VGYDQKQQWP IKNNQHTVEM TLGGGACIIG GDLPARYEA VQLHLHWSNG NDNGSEHSID GRHFAMEMHI VHKKLTSSKE DSKDKFAVLA FMIEVGDKVN KGFQPLVEAL P SISKPHST ...String: WCYEIQTKDP RSSCLGPEKW PGACKENQQS PINIVTARTK VNPRLTPFIL VGYDQKQQWP IKNNQHTVEM TLGGGACIIG GDLPARYEA VQLHLHWSNG NDNGSEHSID GRHFAMEMHI VHKKLTSSKE DSKDKFAVLA FMIEVGDKVN KGFQPLVEAL P SISKPHST STVRESSLQD MLPPSTKMYT YFRYNGSLTT PNCDETVIWT VYKQPIKIHK NQFLEFSKNL YYDEDQKLNM KD NVRPLQP LGKRQVFKS UniProtKB: Carbonic anhydrase 4 |
-Macromolecule #2: Capsid protein VP1
Macromolecule | Name: Capsid protein VP1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Adeno-associated virus 9 |
Molecular weight | Theoretical: 59.295277 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DGVGSSSGNW HCDSQWLGDR VITTSTRTWA LPTYNNHLYK QISNSTSGGS SNDNAYFGYS TPWGYFDFNR FHCHFSPRDW QRLINNNWG FRPKRLNFKL FNIQVKEVTD NNGVKTIANN LTSTVQVFTD SDYQLPYVLG SAHEGCLPPF PADVFMIPQY G YLTLNDGS ...String: DGVGSSSGNW HCDSQWLGDR VITTSTRTWA LPTYNNHLYK QISNSTSGGS SNDNAYFGYS TPWGYFDFNR FHCHFSPRDW QRLINNNWG FRPKRLNFKL FNIQVKEVTD NNGVKTIANN LTSTVQVFTD SDYQLPYVLG SAHEGCLPPF PADVFMIPQY G YLTLNDGS QAVGRSSFYC LEYFPSQMLR TGNNFQFSYE FENVPFHSSY AHSQSLDRLM NPLIDQYLYY LSKTINGSGQ NQ QTLKFSV AGPSNMAVQG RNYIPGPSYR QQRVSTTVTQ NNNSEFAWPG ASSWALNGRN SLMNPGPAMA SHKEGEDRFF PLS GSLIFG KQGTGRDNVD ADKVMITNEE EIKTTNPVAT ESYGQVATNH QSAQWPTSYD AAQAQTGWVQ NQGILPGMVW QDRD VYLQG PIWAKIPHTD GNFHPSPLMG GFGMKHPPPQ ILIKNTPVPA DPPTAFNKDK LNSFITQYST GQVSVEIEWE LQKEN SKRW NPEIQYTSNY YKSNNVEFAV NTEGVYSEPR PIGTRYLTRN L UniProtKB: Capsid protein VP1 |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | |||||||||
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Buffer | pH: 8 Component:
Details: 20mM Tris-Cl, pH8.0; 150mM NaCl. | |||||||||
Grid | Model: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 280 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |