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Yorodumi- EMDB-25655: CryoEM map of anchor 222-1C06 Fab and lateral patch 2B05 Fab bind... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25655 | |||||||||
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Title | CryoEM map of anchor 222-1C06 Fab and lateral patch 2B05 Fab binding H1 HA | |||||||||
Map data | CryoEM map of anchor 222-1C06 Fab and lateral patch 2B05 Fab binding H1 HA | |||||||||
Sample |
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Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Influenza A virus (A/California/04/2009(H1N1)) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.38 Å | |||||||||
Authors | Han J / Ward AB | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nature / Year: 2022 Title: Broadly neutralizing antibodies target a haemagglutinin anchor epitope. Authors: Jenna J Guthmiller / Julianna Han / Henry A Utset / Lei Li / Linda Yu-Ling Lan / Carole Henry / Christopher T Stamper / Meagan McMahon / George O'Dell / Monica L Fernández-Quintero / Alec W ...Authors: Jenna J Guthmiller / Julianna Han / Henry A Utset / Lei Li / Linda Yu-Ling Lan / Carole Henry / Christopher T Stamper / Meagan McMahon / George O'Dell / Monica L Fernández-Quintero / Alec W Freyn / Fatima Amanat / Olivia Stovicek / Lauren Gentles / Sara T Richey / Alba Torrents de la Peña / Victoria Rosado / Haley L Dugan / Nai-Ying Zheng / Micah E Tepora / Dalia J Bitar / Siriruk Changrob / Shirin Strohmeier / Min Huang / Adolfo García-Sastre / Klaus R Liedl / Jesse D Bloom / Raffael Nachbagauer / Peter Palese / Florian Krammer / Lynda Coughlan / Andrew B Ward / Patrick C Wilson / Abstract: Broadly neutralizing antibodies that target epitopes of haemagglutinin on the influenza virus have the potential to provide near universal protection against influenza virus infection. However, viral ...Broadly neutralizing antibodies that target epitopes of haemagglutinin on the influenza virus have the potential to provide near universal protection against influenza virus infection. However, viral mutants that escape broadly neutralizing antibodies have been reported. The identification of broadly neutralizing antibody classes that can neutralize viral escape mutants is critical for universal influenza virus vaccine design. Here we report a distinct class of broadly neutralizing antibodies that target a discrete membrane-proximal anchor epitope of the haemagglutinin stalk domain. Anchor epitope-targeting antibodies are broadly neutralizing across H1 viruses and can cross-react with H2 and H5 viruses that are a pandemic threat. Antibodies that target this anchor epitope utilize a highly restricted repertoire, which encodes two public binding motifs that make extensive contacts with conserved residues in the fusion peptide. Moreover, anchor epitope-targeting B cells are common in the human memory B cell repertoire and were recalled in humans by an oil-in-water adjuvanted chimeric haemagglutinin vaccine, which is a potential universal influenza virus vaccine. To maximize protection against seasonal and pandemic influenza viruses, vaccines should aim to boost this previously untapped source of broadly neutralizing antibodies that are widespread in the human memory B cell pool. | |||||||||
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_25655.map.gz | 118.2 MB | EMDB map data format | |
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Header (meta data) | emd-25655-v30.xml emd-25655.xml | 27.7 KB 27.7 KB | Display Display | EMDB header |
Images | emd_25655.png | 107 KB | ||
Masks | emd_25655_msk_1.map | 125 MB | Mask map | |
Others | emd_25655_half_map_1.map.gz emd_25655_half_map_2.map.gz | 116 MB 116 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25655 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25655 | HTTPS FTP |
-Validation report
Summary document | emd_25655_validation.pdf.gz | 861 KB | Display | EMDB validaton report |
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Full document | emd_25655_full_validation.pdf.gz | 860.5 KB | Display | |
Data in XML | emd_25655_validation.xml.gz | 14 KB | Display | |
Data in CIF | emd_25655_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25655 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25655 | HTTPS FTP |
-Related structure data
Related structure data | 7t3dMC C: citing same article (ref.) M: atomic model generated by this map |
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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_25655.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM map of anchor 222-1C06 Fab and lateral patch 2B05 Fab binding H1 HA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.15 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_25655_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: CryoEM half map of anchor 222-1C06 Fab and...
File | emd_25655_half_map_1.map | ||||||||||||
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Annotation | CryoEM half map of anchor 222-1C06 Fab and lateral patch 2B05 Fab binding H1 HA | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: CryoEM half map of anchor 222-1C06 Fab and...
File | emd_25655_half_map_2.map | ||||||||||||
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Annotation | CryoEM half map of anchor 222-1C06 Fab and lateral patch 2B05 Fab binding H1 HA | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : CryoEM map of anchor 222-1C06 Fab and lateral patch 2B05 Fab bind...
+Supramolecule #1: CryoEM map of anchor 222-1C06 Fab and lateral patch 2B05 Fab bind...
+Supramolecule #2: Monoclonal antibodies 222-1C06 and 2B05
+Supramolecule #3: Hemagglutinin
+Macromolecule #1: Hemagglutinin HA1 chain
+Macromolecule #2: Hemagglutinin HA2 chain
+Macromolecule #3: 2B05 mAb light chain
+Macromolecule #4: 2B05 mAb heavy chain
+Macromolecule #5: 222-1C06 mAb heavy chain
+Macromolecule #6: 222-1C06 mAb light chain
+Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.4 / Details: Tris-buffered saline |
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 49.9 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: 1.8 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 48846 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |