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Yorodumi- EMDB-25634: Negative stain map of monoclonal Fab 047-09 4F04 binding the anch... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25634 | |||||||||
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Title | Negative stain map of monoclonal Fab 047-09 4F04 binding the anchor epitope of H1 HA | |||||||||
Map data | Negative stain map of monoclonal Fab 047-09 4F04 binding the anchor epitope of H1 HA | |||||||||
Sample |
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Keywords | anchor / antibodies / influenza A virus / hemagglutinin / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
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) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 20.0 Å | |||||||||
Authors | Han J / Richey ST / 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_25634.map.gz | 6.1 MB | EMDB map data format | |
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Header (meta data) | emd-25634-v30.xml emd-25634.xml | 13.7 KB 13.7 KB | Display Display | EMDB header |
Images | emd_25634.png | 29.6 KB | ||
Filedesc metadata | emd-25634.cif.gz | 4.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25634 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25634 | HTTPS FTP |
-Validation report
Summary document | emd_25634_validation.pdf.gz | 381.8 KB | Display | EMDB validaton report |
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Full document | emd_25634_full_validation.pdf.gz | 381.4 KB | Display | |
Data in XML | emd_25634_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | emd_25634_validation.cif.gz | 6.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25634 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25634 | HTTPS FTP |
-Related 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_25634.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Negative stain map of monoclonal Fab 047-09 4F04 binding the anchor epitope of H1 HA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Monoclonal Fab 047-09 4F04 binding the anchor epitope of H1 HA
Entire | Name: Monoclonal Fab 047-09 4F04 binding the anchor epitope of H1 HA |
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Components |
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-Supramolecule #1: Monoclonal Fab 047-09 4F04 binding the anchor epitope of H1 HA
Supramolecule | Name: Monoclonal Fab 047-09 4F04 binding the anchor epitope of H1 HA type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) / Strain: A/Michigan/45/2015 H1N1 |
-Supramolecule #2: Monoclonal Fab 047-09 4F04
Supramolecule | Name: Monoclonal Fab 047-09 4F04 / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: Hemagglutinin
Supramolecule | Name: Hemagglutinin / type: complex / ID: 3 / Parent: 1 / Details: Stabilizing mutation E47G in HA2 |
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Source (natural) | Organism: Homo sapiens (human) / Strain: A/California/07/2009 H1N1 |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Details: Tris-buffered saline |
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Staining | Type: NEGATIVE / Material: uranyl formate |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai Spirit / 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: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 2900 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |