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- PDB-8udg: S1V2-72 Fab bound to EHA2 from influenza B/Malaysia/2506/2004 -

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Basic information

Entry
Database: PDB / ID: 8udg
TitleS1V2-72 Fab bound to EHA2 from influenza B/Malaysia/2506/2004
Components
  • Hemagglutinin
  • S1V2-72 heavy chain
  • S1V2-72 light chain
KeywordsVIRAL 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
Haemagglutinin, influenzavirus B / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesInfluenza B virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.98 Å
AuthorsFinney, J. / Kong, S. / Walsh Jr, R.M. / Harrison, S.C. / Kelsoe, G.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI089618 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI155804 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: 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
DepositionSep 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
H: S1V2-72 heavy chain
L: S1V2-72 light chain
M: S1V2-72 heavy chain
N: S1V2-72 light chain


Theoretical massNumber of molelcules
Total (without water)145,2887
Polymers145,2887
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Hemagglutinin


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 S1V2-72 heavy chain


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 S1V2-72 light chain


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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 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
Source (natural)Organism: Influenza B virus (B/Malaysia/2506/2004)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 76.12 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.1particle selection
2SerialEM4.1.0betaimage acquisition
4cryoSPARC4.2.1CTF correction
7UCSF ChimeraXmodel fitting
9cryoSPARC4.2.1initial Euler assignment
10cryoSPARC4.2.1final Euler assignment
11cryoSPARC4.2.1classification
12cryoSPARC4.2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59527 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model

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