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Yorodumi- EMDB-27921: 2H08 Fab in complex with influenza virus neuraminidase from A/Bre... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27921 | |||||||||
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Title | 2H08 Fab in complex with influenza virus neuraminidase from A/Brevig Mission/1/1918 (H1N1) | |||||||||
Map data | sharpened map | |||||||||
Sample |
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Keywords | influenza / monoclonal antibody / NA / H1N1 / cross-reactive antibody / VIRAL PROTEIN | |||||||||
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/Brevig Mission/1/1918(H1N1)) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Turner HL / Ozorowski G / Ward AB | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Immunity / Year: 2023 Title: Human anti-N1 monoclonal antibodies elicited by pandemic H1N1 virus infection broadly inhibit HxN1 viruses in vitro and in vivo. Authors: Lena Hansen / Meagan McMahon / Hannah L Turner / Xueyong Zhu / Jackson S Turner / Gabriel Ozorowski / Daniel Stadlbauer / Juha Vahokoski / Aaron J Schmitz / Amena A Rizk / Wafaa B Alsoussi / ...Authors: Lena Hansen / Meagan McMahon / Hannah L Turner / Xueyong Zhu / Jackson S Turner / Gabriel Ozorowski / Daniel Stadlbauer / Juha Vahokoski / Aaron J Schmitz / Amena A Rizk / Wafaa B Alsoussi / Shirin Strohmeier / Wenli Yu / José Alberto Choreño-Parra / Luis Jiménez-Alvarez / Alfredo Cruz-Lagunas / Joaquín Zúñiga / Philip A Mudd / Rebecca J Cox / Ian A Wilson / Andrew B Ward / Ali H Ellebedy / Florian Krammer / Abstract: Neuraminidase (NA) is one of the two influenza virus surface glycoproteins, and antibodies that target it are an independent correlate of protection. However, our current understanding of NA ...Neuraminidase (NA) is one of the two influenza virus surface glycoproteins, and antibodies that target it are an independent correlate of protection. However, our current understanding of NA antigenicity is incomplete. Here, we describe human monoclonal antibodies (mAbs) from a patient with a pandemic H1N1 virus infection in 2009. Two mAbs exhibited broad reactivity and inhibited NA enzyme activity of seasonal H1N1 viruses circulating before and after 2009, as well as viruses with avian or swine N1s. The mAbs provided robust protection from lethal challenge with human H1N1 and avian H5N1 viruses in mice, and both target an epitope on the lateral face of NA. In summary, we identified two broadly protective NA antibodies that share a novel epitope, inhibited NA activity, and provide protection against virus challenge in mice. Our work reaffirms that NA should be included as a target in future broadly protective or universal influenza virus vaccines. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27921.map.gz | 266.8 MB | EMDB map data format | |
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Header (meta data) | emd-27921-v30.xml emd-27921.xml | 20.5 KB 20.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27921_fsc.xml | 13.9 KB | Display | FSC data file |
Images | emd_27921.png | 128 KB | ||
Masks | emd_27921_msk_1.map | 282.6 MB | Mask map | |
Others | emd_27921_half_map_1.map.gz emd_27921_half_map_2.map.gz | 262.2 MB 262.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27921 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27921 | HTTPS FTP |
-Validation report
Summary document | emd_27921_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_27921_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_27921_validation.xml.gz | 23 KB | Display | |
Data in CIF | emd_27921_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27921 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27921 | HTTPS FTP |
-Related structure data
Related structure data | 8e6kMC 8e6jC 8eqaC 8eqcC 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_27921.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.725 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_27921_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_27921_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_27921_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 2H08 Fab in complex with influenza virus neuraminidase from A/Bre...
Entire | Name: 2H08 Fab in complex with influenza virus neuraminidase from A/Brevig Mission/1/1918 (H1N1) |
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Components |
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-Supramolecule #1: 2H08 Fab in complex with influenza virus neuraminidase from A/Bre...
Supramolecule | Name: 2H08 Fab in complex with influenza virus neuraminidase from A/Brevig Mission/1/1918 (H1N1) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Influenza A virus (A/Brevig Mission/1/1918(H1N1)) |
-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/Brevig Mission/1/1918(H1N1)) / Strain: A/Brevig Mission/1/1918 H1N1 |
Molecular weight | Theoretical: 49.726387 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: ADPHHHHHHS SSDYSDLQRV KQELLEEVKK ELQKVKEEII EAFVQELRKR GSLVPRGSPS RSVILTGNSS LCPISGWAIY SKDNGIRIG SKGDVFVIRE PFISCSHLEC RTFFLTQGAL LNDKHSNGTV KDRSPYRTLM SCPVGEAPSP YNSRFESVAW S ASACHDGM ...String: ADPHHHHHHS SSDYSDLQRV KQELLEEVKK ELQKVKEEII EAFVQELRKR GSLVPRGSPS RSVILTGNSS LCPISGWAIY SKDNGIRIG SKGDVFVIRE PFISCSHLEC RTFFLTQGAL LNDKHSNGTV KDRSPYRTLM SCPVGEAPSP YNSRFESVAW S ASACHDGM GWLTIGISGP DNGAVAVLKY NGIITDTIKS WRNNILRTQE SECACVNGSC FTIMTDGPSN GQASYKILKI EK GKVTKSI ELNAPNYHYE ECSCYPDTGK VMCVCRDNWH GSNRPWVSFD QNLDYQIGYI CSGVFGDNPR PNDGTGSCGP VSS NGANGI KGFSFRYDNG VWIGRTKSTS SRSGFEMIWD PNGWTETDSS FSVRQDIVAI TDWSGYSGSF VQHPELTGLD CMRP CFWVE LIRGQPKENT IWTSGSSISF CGVNSDTVGW SWPDGAELPF SIDK UniProtKB: Neuraminidase |
-Macromolecule #2: 2H08 fragment antigen binding light chain
Macromolecule | Name: 2H08 fragment antigen binding 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: 23.543141 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQMTQSPSS LSASVGDRVT ITCRASQSLS GYLNWYQQKP GKAPKLLIYA TSTLQRGVPS RFSGSGSGTD FTLTISSLQP EDFAIYYCQ QSYSTPPYTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String: DIQMTQSPSS LSASVGDRVT ITCRASQSLS GYLNWYQQKP GKAPKLLIYA TSTLQRGVPS RFSGSGSGTD FTLTISSLQP EDFAIYYCQ QSYSTPPYTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC |
-Macromolecule #3: 2H08 fragment antigen binding heavy chain
Macromolecule | Name: 2H08 fragment antigen binding 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: 23.864762 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLQESGPG LVKPSETLSL TCTVSGDSVS STNYYWGWIR QPPGKGLEWI GSIYYRGITY NSPSLMNRVT ISLDTAKNQF SLNLSSMTA ADTAVYFCAN SIAVSGPLYF HHWGQGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL ...String: QVQLQESGPG LVKPSETLSL TCTVSGDSVS STNYYWGWIR QPPGKGLEWI GSIYYRGITY NSPSLMNRVT ISLDTAKNQF SLNLSSMTA ADTAVYFCAN SIAVSGPLYF HHWGQGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RVEPKSC |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / 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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.2 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number real images: 4126 / Average electron dose: 33.5 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 190000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |