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Open data
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Basic information
Entry | Database: PDB / ID: 9cxt | ||||||||||||||||||||||||||||||
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Title | Hemagglutinin A/Hong Kong/1/68 produced in GnTI- cells | ||||||||||||||||||||||||||||||
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![]() | VIRAL PROTEIN / hemagglutinin / glycoprotein | ||||||||||||||||||||||||||||||
Function / homology | ![]() bioluminescence / viral budding from plasma membrane / generation of precursor metabolites and energy / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / 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 ...bioluminescence / viral budding from plasma membrane / generation of precursor metabolites and energy / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / 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: 3.4 Å | ||||||||||||||||||||||||||||||
![]() | Torrents de la Pena, A. / de Paiva Froes Rocha, R. / Ward, A.B. | ||||||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and immunological characterization of the H3 influenza hemagglutinin during antigenic drift Authors: de Paiva Froes Rocha, R. / Torrents de la Pena, A. / Ward, A.B. / de Vries, R.P. / Berndsen, Z.T. / Chakraborty, S. | ||||||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 312.8 KB | Display | ![]() |
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PDB format | ![]() | 240.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 57.5 KB | Display | |
Data in CIF | ![]() | 83.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 45997MC ![]() 9cxuC ![]() 9d0yC ![]() 9d1uC ![]() 9d2mC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 38523.496 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: ![]() #2: Protein | Mass: 56073.738 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA, GFP / Production host: ![]() #3: Sugar | ChemComp-NAG / Has ligand of interest | N | Has protein modification | Y | |
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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: hemagglutinin A/Hong Kong/1/68 trimer / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.4 / Details: TBS |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm |
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
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59301 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 4ZCJ Accession code: 4ZCJ / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refine LS restraints |
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