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- PDB-6hjn: Structure of Influenza Hemagglutinin ectodomain (A/duck/Alberta/35/76) -
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Open data
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Basic information
Entry | Database: PDB / ID: 6hjn | ||||||||||||||||||||||||
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Title | Structure of Influenza Hemagglutinin ectodomain (A/duck/Alberta/35/76) | ||||||||||||||||||||||||
![]() | (Hemagglutinin) x 2 | ||||||||||||||||||||||||
![]() | VIRAL PROTEIN / Influenza virus / Hemagglutinin / Membrane protein / Membrane fusion | ||||||||||||||||||||||||
Function / homology | ![]() 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 / membrane Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||||||||||||||
![]() | Benton, D.J. / Rosenthal, P.B. | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Influenza hemagglutinin membrane anchor. Authors: Donald J Benton / Andrea Nans / Lesley J Calder / Jack Turner / Ursula Neu / Yi Pu Lin / Esther Ketelaars / Nicole L Kallewaard / Davide Corti / Antonio Lanzavecchia / Steven J Gamblin / ...Authors: Donald J Benton / Andrea Nans / Lesley J Calder / Jack Turner / Ursula Neu / Yi Pu Lin / Esther Ketelaars / Nicole L Kallewaard / Davide Corti / Antonio Lanzavecchia / Steven J Gamblin / Peter B Rosenthal / John J Skehel / ![]() ![]() ![]() Abstract: Viruses with membranes fuse them with cellular membranes, to transfer their genomes into cells at the beginning of infection. For Influenza virus, the membrane glycoprotein involved in fusion is the ...Viruses with membranes fuse them with cellular membranes, to transfer their genomes into cells at the beginning of infection. For Influenza virus, the membrane glycoprotein involved in fusion is the hemagglutinin (HA), the 3D structure of which is known from X-ray crystallographic studies. The soluble ectodomain fragments used in these studies lacked the "membrane anchor" portion of the molecule. Since this region has a role in membrane fusion, we have determined its structure by analyzing the intact, full-length molecule in a detergent micelle, using cryo-EM. We have also compared the structures of full-length HA-detergent micelles with full-length HA-Fab complex detergent micelles, to describe an infectivity-neutralizing monoclonal Fab that binds near the ectodomain membrane anchor junction. We determine a high-resolution HA structure which compares favorably in detail with the structure of the ectodomain seen by X-ray crystallography; we detect, clearly, all five carbohydrate side chains of HA; and we find that the ectodomain is joined to the membrane anchor by flexible, eight-residue-long, linkers. The linkers extend into the detergent micelle to join a central triple-helical structure that is a major component of the membrane anchor. | ||||||||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 304 KB | Display | ![]() |
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PDB format | ![]() | 253.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 0234MC ![]() 0235C ![]() 0236C ![]() 0237C ![]() 6hjpC ![]() 6hjqC ![]() 6hjrC ![]() 6hkgC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 35571.695 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q9WCE0, UniProt: P26562*PLUS #2: Protein | Mass: 19838.834 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: P26562 |
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-Sugars , 4 types, 15 molecules
#3: 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 #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 1 types, 3 molecules ![](data/chem/img/UPL.gif)
#7: Chemical |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: A/duck/Alberta/35/76 Hemagglutinin Ectodomain / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL | ||||||||||||||||||||||||||||
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Molecular weight | Value: 0.17 MDa / Experimental value: NO | ||||||||||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE |
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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 / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 43 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 20 |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: C3 (3 fold cyclic) |
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 365887 / Symmetry type: POINT |