+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20594 | |||||||||
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Title | CryoEM-derived model of NA-63 Fab in complex with N9 Shanghai2 | |||||||||
Map data | CryoEM map of N9 Shanghai2 in complex with Fab-63 | |||||||||
Sample |
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Function / homology | Function and homology information 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 | Influenza A virus (A/environment/Shanghai/S1439/2013(H7N9)) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.05 Å | |||||||||
Authors | Ward AB / Turner HL | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Cell Host Microbe / Year: 2019 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20594.map.gz | 117.5 MB | EMDB map data format | |
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Header (meta data) | emd-20594-v30.xml emd-20594.xml | 20.7 KB 20.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20594_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_20594.png | 96.3 KB | ||
Masks | emd_20594_msk_1.map | 125 MB | Mask map | |
Others | emd_20594_half_map_1.map.gz emd_20594_half_map_2.map.gz | 115.2 MB 115.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20594 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20594 | HTTPS FTP |
-Validation report
Summary document | emd_20594_validation.pdf.gz | 816.3 KB | Display | EMDB validaton report |
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Full document | emd_20594_full_validation.pdf.gz | 815.9 KB | Display | |
Data in XML | emd_20594_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | emd_20594_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20594 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20594 | HTTPS FTP |
-Related structure data
Related structure data | 6u02MC 6pzdC 6pzeC 6pzfC 6pzgC 6pzhC 6pzwC 6pzyC 6pzzC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_20594.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM map of N9 Shanghai2 in complex with Fab-63 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
File | emd_20594_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map A of N9 Shanghai2 in complex with Fab-63
File | emd_20594_half_map_1.map | ||||||||||||
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Annotation | Half map A of N9 Shanghai2 in complex with Fab-63 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B of N9 Shanghai2 in complex with Fab-63
File | emd_20594_half_map_2.map | ||||||||||||
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Annotation | Half map B of N9 Shanghai2 in complex with Fab-63 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : NA-63 Fab in complex with N9 Shanghai2
Entire | Name: NA-63 Fab in complex with N9 Shanghai2 |
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Components |
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-Supramolecule #1: NA-63 Fab in complex with N9 Shanghai2
Supramolecule | Name: NA-63 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: Influenza A virus (A/environment/Shanghai/S1439/2013(H7N9)) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-Supramolecule #3: NA-63 Fab
Supramolecule | Name: NA-63 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Cricetinae gen. sp. (mammal) |
-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: Influenza A virus (A/environment/Shanghai/S1439/2013(H7N9)) Strain: A/environment/Shanghai/S1439/2013(H7N9) |
Molecular weight | Theoretical: 48.214508 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
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: Fab-63 Light Chain
Macromolecule | Name: Fab-63 Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.432014 KDa |
Recombinant expression | Organism: Cricetinae gen. sp. (mammal) |
Sequence | String: DIVMTQSPSS LSASVGDRVT ITCRASQSIS TYLNWYQQKP GKAPKLLIYA ASSLQGGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSYSTPLYTF GQGTKLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String: DIVMTQSPSS LSASVGDRVT ITCRASQSIS TYLNWYQQKP GKAPKLLIYA ASSLQGGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSYSTPLYTF GQGTKLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC |
-Macromolecule #3: Fab-63 Heavy Chain
Macromolecule | Name: Fab-63 Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.547318 KDa |
Recombinant expression | Organism: Cricetinae gen. sp. (mammal) |
Sequence | String: EVQLVESGGG LVQPGGSLRL SCAASGFTFS SYWMSWVRQA PGKGLDWVAN IKQDGSEKYY VDSVKGRFTI SRHNAKNSLY LQMNSLRAE DTAVYYCASS TAAEFFDYWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV ...String: EVQLVESGGG LVQPGGSLRL SCAASGFTFS SYWMSWVRQA PGKGLDWVAN IKQDGSEKYY VDSVKGRFTI SRHNAKNSLY LQMNSLRAE DTAVYYCASS TAAEFFDYWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKRVEP KSC |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / 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
Concentration | 0.14 mg/mL |
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Buffer | pH: 7.4 |
Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-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 exposure time: 8.25 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |