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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-20540 | |||||||||
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Title | CryoEM map of NA-73 Fab in complex with N9 Shanghai2 | |||||||||
![]() | CryoEM map of NA-73 Fab in complex with N9 Shanghai | |||||||||
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Function / homology | ![]() exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.17 Å | |||||||||
![]() | Ward AB / Turner HL / Zhu X | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis of Protection against H7N9 Influenza Virus by Human Anti-N9 Neuraminidase Antibodies. Authors: Xueyong Zhu / Hannah L Turner / Shanshan Lang / Ryan McBride / Sandhya Bangaru / Iuliia M Gilchuk / Wenli Yu / James C Paulson / James E Crowe / Andrew B Ward / Ian A Wilson / ![]() Abstract: Influenza virus neuraminidase (NA) is a major target for small-molecule antiviral drugs. Antibodies targeting the NA surface antigen could also inhibit virus entry and egress to provide host ...Influenza virus neuraminidase (NA) is a major target for small-molecule antiviral drugs. Antibodies targeting the NA surface antigen could also inhibit virus entry and egress to provide host protection. However, our understanding of the nature and range of target epitopes is limited because of a lack of human antibody structures with influenza neuraminidase. Here, we describe crystal and cryogenic electron microscopy (cryo-EM) structures of NAs from human-infecting avian H7N9 viruses in complex with five human anti-N9 antibodies, systematically defining several antigenic sites and antibody epitope footprints. These antibodies either fully or partially block the NA active site or bind to epitopes distant from the active site while still showing neuraminidase inhibition. The inhibition of antibodies to NAs was further analyzed by glycan array and solution-based NA activity assays. Together, these structural studies provide insights into protection by anti-NA antibodies and templates for the development of NA-based influenza virus vaccines and therapeutics. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 31.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.3 KB 20.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.1 KB | Display | ![]() |
Images | ![]() | 137.2 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Others | ![]() ![]() | 58.8 MB 58.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 846.8 KB | Display | ![]() |
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Full document | ![]() | 846.3 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 21.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6pzyMC ![]() 6pzdC ![]() 6pzeC ![]() 6pzfC ![]() 6pzgC ![]() 6pzhC ![]() 6pzwC ![]() 6pzzC ![]() 6u02C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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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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Annotation | CryoEM map of NA-73 Fab in complex with N9 Shanghai | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: Halfmap A of CryoEM map of NA-73 Fab in complex with N9 Shanghai
File | emd_20540_half_map_1.map | ||||||||||||
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Annotation | Halfmap A of CryoEM map of NA-73 Fab in complex with N9 Shanghai | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Halfmap B of CryoEM map of NA-73 Fab in complex with N9 Shanghai
File | emd_20540_half_map_2.map | ||||||||||||
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Annotation | Halfmap B of CryoEM map of NA-73 Fab in complex with N9 Shanghai | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : NA-73 Fab in complex with N9 Shanghai2
Entire | Name: NA-73 Fab in complex with N9 Shanghai2 |
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Components |
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-Supramolecule #1: NA-73 Fab in complex with N9 Shanghai2
Supramolecule | Name: NA-73 Fab in complex with N9 Shanghai2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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-Supramolecule #2: N9 Shanghai2
Supramolecule | Name: N9 Shanghai2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Supramolecule #3: NA-73 Fab
Supramolecule | Name: NA-73 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Neuraminidase
Macromolecule | Name: Neuraminidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: exo-alpha-sialidase |
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Source (natural) | Organism: ![]() Strain: A/environment/Shanghai/S1439/2013(H7N9) |
Molecular weight | Theoretical: 48.214508 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: LKPGCNCSHS QPETTNTSQT IINNYYNETN ITNIQMEERT SRNFNNLTKG LCTINSWHIY GKDNAVRIGE SSDVLVTREP YVSCDPDEC RFYALSQGTT IRGKHSNGTI HDRSQYRALI SWPLSSPPTV YNSRVECIGW SSTSCHDGKS RMSICISGPN N NASAVVWY ...String: LKPGCNCSHS QPETTNTSQT IINNYYNETN ITNIQMEERT SRNFNNLTKG LCTINSWHIY GKDNAVRIGE SSDVLVTREP YVSCDPDEC RFYALSQGTT IRGKHSNGTI HDRSQYRALI SWPLSSPPTV YNSRVECIGW SSTSCHDGKS RMSICISGPN N NASAVVWY NRRPVAEINT WARNILRTQE SECVCHNGVC PVVFTDGSAT GPADTRIYYF KEGKILKWES LTGTAKHIEE CS CYGERTG ITCTCRDNWQ GSNRPVIQID PVAMTHTSQY ICSPVLTDNP RPNDPNIGKC NDPYPGNNNN GVKGFSYLDG ANT WLGRTI STASRSGYEM LKVPNALTDD RSKPIQGQTI VLNADWSGYS GSFMDYWAEG DCYRACFYVE LIRGRPKEDK VWWT SNSIV SMCSSTEFLG QWNWPDGAKI EYFL |
-Macromolecule #2: NA-73 fragment antibody heavy chain
Macromolecule | Name: NA-73 fragment antibody heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 24.822797 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: QVQLEESGPG LVKPSETLSL TCTVSGYTIS SGYYWGWIRQ PPGKGLEWIG CNNHRGSSYY NPSLKSRVII SVDTTKNKFS LKLSSVTAA DTAVYYCARD PSFWSSTSRT SPYYYGMDVW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFPEPVTV ...String: QVQLEESGPG LVKPSETLSL TCTVSGYTIS SGYYWGWIRQ PPGKGLEWIG CNNHRGSSYY NPSLKSRVII SVDTTKNKFS LKLSSVTAA DTAVYYCARD PSFWSSTSRT SPYYYGMDVW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFPEPVTV SWNSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKRVE PKSC |
-Macromolecule #3: NA-73 fragment antibody light chain
Macromolecule | Name: NA-73 fragment antibody light chain / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 22.792084 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: QSVLTQPPSA SGTPGQRVTI SCSGSSSNIG INTVNWYQQL PGTAPKLLIY SNNQRPSGVP DRFSGSKSGT SASLAISGLQ SEDEADYYC AAWDDNLNGW VFGGGTKLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String: QSVLTQPPSA SGTPGQRVTI SCSGSSSNIG INTVNWYQQL PGTAPKLLIY SNNQRPSGVP DRFSGSKSGT SASLAISGLQ SEDEADYYC AAWDDNLNGW VFGGGTKLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS |
-Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 4 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.14 mg/mL |
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Buffer | pH: 7.4 |
Grid | Pretreatment - Type: GLOW DISCHARGE / Details: unspecified |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |