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Yorodumi- EMDB-9029: Hemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in co... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9029 | |||||||||
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Title | Hemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in complex with Fab from IgG CR9114 and single-domain antibody SD84 | |||||||||
Map data | Hemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in complex with Fab from IgG CR9114 and single-domain antibody SD84 | |||||||||
Sample |
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Biological species | Influenza B virus (B/Massachusetts/02/2012) / Homo sapiens (human) / Lama glama (llama) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.9 Å | |||||||||
Authors | Pallesen J / Nieusma T / Hoffman RMB / Ward AB | |||||||||
Citation | Journal: Science / Year: 2018 Title: Universal protection against influenza infection by a multidomain antibody to influenza hemagglutinin. Authors: Nick S Laursen / Robert H E Friesen / Xueyong Zhu / Mandy Jongeneelen / Sven Blokland / Jan Vermond / Alida van Eijgen / Chan Tang / Harry van Diepen / Galina Obmolova / Marijn van der Neut ...Authors: Nick S Laursen / Robert H E Friesen / Xueyong Zhu / Mandy Jongeneelen / Sven Blokland / Jan Vermond / Alida van Eijgen / Chan Tang / Harry van Diepen / Galina Obmolova / Marijn van der Neut Kolfschoten / David Zuijdgeest / Roel Straetemans / Ryan M B Hoffman / Travis Nieusma / Jesper Pallesen / Hannah L Turner / Steffen M Bernard / Andrew B Ward / Jinquan Luo / Leo L M Poon / Anna P Tretiakova / James M Wilson / Maria P Limberis / Ronald Vogels / Boerries Brandenburg / Joost A Kolkman / Ian A Wilson / Abstract: Broadly neutralizing antibodies against highly variable pathogens have stimulated the design of vaccines and therapeutics. We report the use of diverse camelid single-domain antibodies to influenza ...Broadly neutralizing antibodies against highly variable pathogens have stimulated the design of vaccines and therapeutics. We report the use of diverse camelid single-domain antibodies to influenza virus hemagglutinin to generate multidomain antibodies with impressive breadth and potency. Multidomain antibody MD3606 protects mice against influenza A and B infection when administered intravenously or expressed locally from a recombinant adeno-associated virus vector. Crystal and single-particle electron microscopy structures of these antibodies with hemagglutinins from influenza A and B viruses reveal binding to highly conserved epitopes. Collectively, our findings demonstrate that multidomain antibodies targeting multiple epitopes exhibit enhanced virus cross-reactivity and potency. In combination with adeno-associated virus-mediated gene delivery, they may provide an effective strategy to prevent infection with influenza virus and other highly variable pathogens. | |||||||||
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_9029.map.gz | 42.4 MB | EMDB map data format | |
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Header (meta data) | emd-9029-v30.xml emd-9029.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9029_fsc.xml | 7.9 KB | Display | FSC data file |
Images | emd_9029.png | 72.4 KB | ||
Others | emd_9029_half_map_1.map.gz emd_9029_half_map_2.map.gz | 35 MB 35 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9029 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9029 | HTTPS FTP |
-Validation report
Summary document | emd_9029_validation.pdf.gz | 78.3 KB | Display | EMDB validaton report |
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Full document | emd_9029_full_validation.pdf.gz | 77.4 KB | Display | |
Data in XML | emd_9029_validation.xml.gz | 492 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9029 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9029 | HTTPS FTP |
-Related structure data
Related structure data | 6ck8C 6cnvC 6cnwC 6fysC 6fytC 6fyuC 6fywC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_9029.map.gz / Format: CCP4 / Size: 45.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Hemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in complex with Fab from IgG CR9114 and single-domain antibody SD84 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Hemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in complex with Fab...
File | emd_9029_half_map_1.map | ||||||||||||
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Annotation | Hemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in complex with Fab from IgG CR9114 and single-domain antibody SD84, half map #1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Hemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in complex with Fab...
File | emd_9029_half_map_2.map | ||||||||||||
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Annotation | Hemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in complex with Fab from IgG CR9114 and single-domain antibody SD84, half map #2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Hemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in co...
Entire | Name: Hemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in complex with Fab from IgG CR9114 and single-domain antibody SD84. |
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Components |
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-Supramolecule #1: Hemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in co...
Supramolecule | Name: Hemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in complex with Fab from IgG CR9114 and single-domain antibody SD84. type: complex / ID: 1 / Parent: 0 |
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Molecular weight | Theoretical: 400 KDa |
-Supramolecule #2: Hemagglutinin trimeric ectodomain
Supramolecule | Name: Hemagglutinin trimeric ectodomain / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Influenza B virus (B/Massachusetts/02/2012) / Strain: (B/Massachusetts/02/2012) |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #3: Fab from IgG CR9114
Supramolecule | Name: Fab from IgG CR9114 / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 50 KDa |
-Supramolecule #4: Single-domain antibody SD84
Supramolecule | Name: Single-domain antibody SD84 / type: complex / ID: 4 / Parent: 1 |
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Source (natural) | Organism: Lama glama (llama) |
Recombinant expression | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 25 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 47.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |