+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26319 | |||||||||
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Title | Influenza Neuraminidase N1-MI15-sNAp-174 | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Influenza A virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.25 Å | |||||||||
Authors | Acton OJ / Veesler D / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structure-based design of stabilized recombinant influenza neuraminidase tetramers. Authors: Daniel Ellis / Julia Lederhofer / Oliver J Acton / Yaroslav Tsybovsky / Sally Kephart / Christina Yap / Rebecca A Gillespie / Adrian Creanga / Audrey Olshefsky / Tyler Stephens / Deleah ...Authors: Daniel Ellis / Julia Lederhofer / Oliver J Acton / Yaroslav Tsybovsky / Sally Kephart / Christina Yap / Rebecca A Gillespie / Adrian Creanga / Audrey Olshefsky / Tyler Stephens / Deleah Pettie / Michael Murphy / Claire Sydeman / Maggie Ahlrichs / Sidney Chan / Andrew J Borst / Young-Jun Park / Kelly K Lee / Barney S Graham / David Veesler / Neil P King / Masaru Kanekiyo / Abstract: Influenza virus neuraminidase (NA) is a major antiviral drug target and has recently reemerged as a key target of antibody-mediated protective immunity. Here we show that recombinant NAs across non- ...Influenza virus neuraminidase (NA) is a major antiviral drug target and has recently reemerged as a key target of antibody-mediated protective immunity. Here we show that recombinant NAs across non-bat subtypes adopt various tetrameric conformations, including an "open" state that may help explain poorly understood variations in NA stability across viral strains and subtypes. We use homology-directed protein design to uncover the structural principles underlying these distinct tetrameric conformations and stabilize multiple recombinant NAs in the "closed" state, yielding two near-atomic resolution structures of NA by cryo-EM. In addition to enhancing thermal stability, conformational stabilization improves affinity to protective antibodies elicited by viral infection, including antibodies targeting a quaternary epitope and the broadly conserved catalytic site. Stabilized NAs can also be integrated into viruses without affecting fitness. Our findings provide a deeper understanding of NA structure, stability, and antigenicity, and establish design strategies for reinforcing the conformational integrity of recombinant NA proteins. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26319.map.gz | 1.7 MB | EMDB map data format | |
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Header (meta data) | emd-26319-v30.xml emd-26319.xml | 14.4 KB 14.4 KB | Display Display | EMDB header |
Images | emd_26319.png | 68.5 KB | ||
Others | emd_26319_additional_1.map.gz | 16.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26319 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26319 | HTTPS FTP |
-Validation report
Summary document | emd_26319_validation.pdf.gz | 336.3 KB | Display | EMDB validaton report |
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Full document | emd_26319_full_validation.pdf.gz | 335.9 KB | Display | |
Data in XML | emd_26319_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_26319_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26319 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26319 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_26319.map.gz / Format: CCP4 / Size: 32.4 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: 1.16 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_26319_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Structure-based design of an engineered Influenza Neuraminidase t...
Entire | Name: Structure-based design of an engineered Influenza Neuraminidase tetramer |
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Components |
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-Supramolecule #1: Structure-based design of an engineered Influenza Neuraminidase t...
Supramolecule | Name: Structure-based design of an engineered Influenza Neuraminidase tetramer type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Influenza A virus |
Recombinant expression | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 210 kDa/nm |
-Macromolecule #1: Influenza N1-MI15-sNAp-174
Macromolecule | Name: Influenza N1-MI15-sNAp-174 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Influenza A virus |
Molecular weight | Theoretical: 42.577742 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: VKLAGNSSLC PVSGWAPLSK DNSVRIGSKG DVFVIREPFI SCSPLECRQF FLTQGALLND KHSNGTIKDR SPYRTLMSVP IGSVPSPYN ARFESIAWSA SACHDGINWL TIGITGPDSG AVAILKYNGI ITDTIKSWRN NILRTQESEC ACVNGSCFTI M TDGPSDGQ ...String: VKLAGNSSLC PVSGWAPLSK DNSVRIGSKG DVFVIREPFI SCSPLECRQF FLTQGALLND KHSNGTIKDR SPYRTLMSVP IGSVPSPYN ARFESIAWSA SACHDGINWL TIGITGPDSG AVAILKYNGI ITDTIKSWRN NILRTQESEC ACVNGSCFTI M TDGPSDGQ ASYKIFRIEK GKIIKSVEMK APNYHYEECS CYPDSSEITC VCRDNWHGSN RPWVSFNQNL EYQMGYICSG VF GDNPRPN DKTGSCGPVS SNGANGVKGF SFKYGNGVWI GRTKSISSRK GFEMIWDPNG WTGTDNKFSI KQDIVGINEW SGY SGSFVM HPELTGLDCI VPCFWVELIR GRPEENTIWT SGSSISFCGV NSDTVGWSWP DGAELPFTID K |
-Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 8 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 36000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
-Image processing
Final reconstruction | Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 72106 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |