+Open data
-Basic information
Entry | Database: PDB / ID: 8udg | ||||||||||||
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Title | S1V2-72 Fab bound to EHA2 from influenza B/Malaysia/2506/2004 | ||||||||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / immunoglobulin / complex / hemagglutinin / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||||||||
Function / homology | Function and homology information viral budding from plasma membrane / endocytosis involved in viral entry into 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 Similarity search - Function | ||||||||||||
Biological species | Influenza B virus Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.98 Å | ||||||||||||
Authors | Finney, J. / Kong, S. / Walsh Jr, R.M. / Harrison, S.C. / Kelsoe, G. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2024 Title: Protective human antibodies against a conserved epitope in pre- and postfusion influenza hemagglutinin. Authors: Joel Finney / Annie Park Moseman / Susan Kong / Akiko Watanabe / Shengli Song / Richard M Walsh / Masayuki Kuraoka / Ryutaro Kotaki / E Ashley Moseman / Kevin R McCarthy / Dongmei Liao / ...Authors: Joel Finney / Annie Park Moseman / Susan Kong / Akiko Watanabe / Shengli Song / Richard M Walsh / Masayuki Kuraoka / Ryutaro Kotaki / E Ashley Moseman / Kevin R McCarthy / Dongmei Liao / Xiaoe Liang / Xiaoyan Nie / Olivia Lavidor / Richard Abbott / Stephen C Harrison / Garnett Kelsoe / Abstract: Phylogenetically and antigenically distinct influenza A and B viruses (IAV and IBV) circulate in human populations, causing widespread morbidity. Antibodies (Abs) that bind epitopes conserved in both ...Phylogenetically and antigenically distinct influenza A and B viruses (IAV and IBV) circulate in human populations, causing widespread morbidity. Antibodies (Abs) that bind epitopes conserved in both IAV and IBV hemagglutinins (HAs) could protect against disease by diverse virus subtypes. Only one reported HA Ab, isolated from a combinatorial display library, protects against both IAV and IBV. Thus, there has been so far no information on the likelihood of finding naturally occurring human Abs that bind HAs of diverse IAV subtypes and IBV lineages. We have now recovered from several unrelated human donors five clonal Abs that bind a conserved epitope preferentially exposed in the postfusion conformation of IAV and IVB HA2. These Abs lack neutralizing activity in vitro but in mice provide strong, IgG subtype-dependent protection against lethal IAV and IBV infections. Strategies to elicit similar Abs routinely might contribute to more effective influenza vaccines. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8udg.cif.gz | 407.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8udg.ent.gz | 340.3 KB | Display | PDB format |
PDBx/mmJSON format | 8udg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8udg_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8udg_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8udg_validation.xml.gz | 46 KB | Display | |
Data in CIF | 8udg_validation.cif.gz | 69.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/8udg ftp://data.pdbj.org/pub/pdb/validation_reports/ud/8udg | HTTPS FTP |
-Related structure data
Related structure data | 42149MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 17169.160 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza B virus (B/Malaysia/2506/2004) Gene: HA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2S1PX21 #2: Protein | Mass: 24135.121 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Antibody | Mass: 22755.045 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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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 |
-Sample preparation
Component | Name: Complex of two S1V2-72 Fabs with postfusion HA2 / Type: COMPLEX Details: Fab fragment generated by proteolytic cleavage of S1V2-72 IgG Entity ID: #2-#3, #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Influenza B virus (B/Malaysia/2506/2004) |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: BL21(DE3) |
Buffer solution | pH: 7.4 |
Specimen | 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: Quantifoil R0.6/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 76.12 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59527 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model |