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Yorodumi- EMDB-6332: 3D reconstruction of a ferritin-based nanoparticle displaying H1 ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6332 | |||||||||
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Title | 3D reconstruction of a ferritin-based nanoparticle displaying H1 Hemagglutinin stem epitopes | |||||||||
Map data | ferritin-hemagglutinin nanoparticle | |||||||||
Sample |
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Keywords | nanoparticle / vaccine / epitope display / influenza | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 16.0 Å | |||||||||
Authors | Gallagher JR / Harris AK / Yassine HM / Boyington JC / McTamney PM / Wei CJ / Masaru M / Kong WP / Wang L / Zhang Y ...Gallagher JR / Harris AK / Yassine HM / Boyington JC / McTamney PM / Wei CJ / Masaru M / Kong WP / Wang L / Zhang Y / Joyce MG / Lingwood D / Moin SM / Andersen H / Okuno Y / Rao SS / Kwong PD / Mascola JR / Nabel GJ / Graham BS | |||||||||
Citation | Journal: Nat Med / Year: 2015 Title: Hemagglutinin-stem nanoparticles generate heterosubtypic influenza protection. Authors: Hadi M Yassine / Jeffrey C Boyington / Patrick M McTamney / Chih-Jen Wei / Masaru Kanekiyo / Wing-Pui Kong / John R Gallagher / Lingshu Wang / Yi Zhang / M Gordon Joyce / Daniel Lingwood / ...Authors: Hadi M Yassine / Jeffrey C Boyington / Patrick M McTamney / Chih-Jen Wei / Masaru Kanekiyo / Wing-Pui Kong / John R Gallagher / Lingshu Wang / Yi Zhang / M Gordon Joyce / Daniel Lingwood / Syed M Moin / Hanne Andersen / Yoshinobu Okuno / Srinivas S Rao / Audray K Harris / Peter D Kwong / John R Mascola / Gary J Nabel / Barney S Graham / Abstract: The antibody response to influenza is primarily focused on the head region of the hemagglutinin (HA) glycoprotein, which in turn undergoes antigenic drift, thus necessitating annual updates of ...The antibody response to influenza is primarily focused on the head region of the hemagglutinin (HA) glycoprotein, which in turn undergoes antigenic drift, thus necessitating annual updates of influenza vaccines. In contrast, the immunogenically subdominant stem region of HA is highly conserved and recognized by antibodies capable of binding multiple HA subtypes. Here we report the structure-based development of an H1 HA stem-only immunogen that confers heterosubtypic protection in mice and ferrets. Six iterative cycles of structure-based design (Gen1-Gen6) yielded successive H1 HA stabilized-stem (HA-SS) immunogens that lack the immunodominant head domain. Antigenic characterization, determination of two HA-SS crystal structures in complex with stem-specific monoclonal antibodies and cryo-electron microscopy analysis of HA-SS on ferritin nanoparticles (H1-SS-np) confirmed the preservation of key structural elements. Vaccination of mice and ferrets with H1-SS-np elicited broadly cross-reactive antibodies that completely protected mice and partially protected ferrets against lethal heterosubtypic H5N1 influenza virus challenge despite the absence of detectable H5N1 neutralizing activity in vitro. Passive transfer of immunoglobulin from H1-SS-np-immunized mice to naive mice conferred protection against H5N1 challenge, indicating that vaccine-elicited HA stem-specific antibodies can protect against diverse group 1 influenza strains. | |||||||||
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_6332.map.gz | 7 MB | EMDB map data format | |
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Header (meta data) | emd-6332-v30.xml emd-6332.xml | 13.6 KB 13.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6332_fsc.xml | 5.4 KB | Display | FSC data file |
Images | emd_6332.png | 124.6 KB | ||
Masks | emd_6332_msk_1.map | 8 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6332 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6332 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6332.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | ferritin-hemagglutinin nanoparticle | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.63 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Segmentation: relion postprocess automask: threshold=0.008 extend=4, soft-edge=8,
Annotation | relion_postprocess automask: threshold=0.008 extend=4, soft-edge=8, | ||||||||||||
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File | emd_6332_msk_1.map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : H. pylori ferritin fusion with engineered H1 hemagglutin stem domain
Entire | Name: H. pylori ferritin fusion with engineered H1 hemagglutin stem domain |
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Components |
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-Supramolecule #1000: H. pylori ferritin fusion with engineered H1 hemagglutin stem domain
Supramolecule | Name: H. pylori ferritin fusion with engineered H1 hemagglutin stem domain type: sample / ID: 1000 / Oligomeric state: nanoparticle of 24 subunits / Number unique components: 1 |
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Molecular weight | Experimental: 1 MDa / Theoretical: 970 KDa / Method: gel filtration |
-Macromolecule #1: Hemagglutinin stem ferritin nanoparticle
Macromolecule | Name: Hemagglutinin stem ferritin nanoparticle / type: protein_or_peptide / ID: 1 / Name.synonym: HA-stem ferritin nanoparticle / Number of copies: 24 / Oligomeric state: nanoparticle of 24 subunits / Recombinant expression: Yes |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Experimental: 1 MDa / Theoretical: 970 KDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: 293F |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.8 mg/mL |
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Buffer | pH: 7.4 / Details: 12 mM Na/K phosphate, 137 mM NaCl |
Grid | Details: holey carbon film, Quantifoil |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 118 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 7.0 µm / Nominal defocus min: 3.5 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Temperature | Min: 80 K / Max: 105 K / Average: 100 K |
Date | Oct 1, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 209 / Average electron dose: 15 e/Å2 / Bits/pixel: 16 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |