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- PDB-8ct6: 1F8 mAb in complex with the computationally optimized broadly rea... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ct6 | ||||||
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Title | 1F8 mAb in complex with the computationally optimized broadly reactive H1 influenza hemagglutinin P1 | ||||||
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Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dzimianski, J.V. / DuBois, R.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into the broad protection against H1 influenza viruses by a computationally optimized hemagglutinin vaccine. Authors: John V Dzimianski / Julianna Han / Giuseppe A Sautto / Sara M O'Rourke / Joseph M Cruz / Spencer R Pierce / Jeffrey W Ecker / Michael A Carlock / Kaito A Nagashima / Jarrod J Mousa / Ted M ...Authors: John V Dzimianski / Julianna Han / Giuseppe A Sautto / Sara M O'Rourke / Joseph M Cruz / Spencer R Pierce / Jeffrey W Ecker / Michael A Carlock / Kaito A Nagashima / Jarrod J Mousa / Ted M Ross / Andrew B Ward / Rebecca M DuBois / ![]() Abstract: Influenza virus poses an ongoing human health threat with pandemic potential. Due to mutations in circulating strains, formulating effective vaccines remains a challenge. The use of computationally ...Influenza virus poses an ongoing human health threat with pandemic potential. Due to mutations in circulating strains, formulating effective vaccines remains a challenge. The use of computationally optimized broadly reactive antigen (COBRA) hemagglutinin (HA) proteins is a promising vaccine strategy to protect against a wide range of current and future influenza viruses. Though effective in preclinical studies, the mechanistic basis driving the broad reactivity of COBRA proteins remains to be elucidated. Here, we report the crystal structure of the COBRA HA termed P1 and identify antigenic and glycosylation properties that contribute to its immunogenicity. We further report the cryo-EM structure of the P1-elicited broadly neutralizing antibody 1F8 bound to COBRA P1, revealing 1F8 to recognize an atypical receptor binding site epitope via an unexpected mode of binding. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 413.1 KB | Display | ![]() |
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PDB format | ![]() | 307.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein , 1 types, 3 molecules BAC
#1: Protein | Mass: 63264.535 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-Antibody , 2 types, 4 molecules LKHJ
#2: Antibody | Mass: 23918.271 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #3: Antibody | Mass: 23900.818 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Sugars , 4 types, 14 molecules ![](data/chem/img/NAG.gif)
#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source | ||
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#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source | ||
#6: Polysaccharide | ![]() #7: Sugar | ChemComp-NAG / ![]() |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 / Details: TBS | ||||||||||||||||||||||||||||
Specimen | Conc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | ||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||
Vitrification![]() | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||
3D reconstruction![]() | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57151 / Symmetry type: POINT | |||||||||
Refinement | Cross valid method: NONE |