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- PDB-8e6k: 2H08 Fab in complex with influenza virus neuraminidase from A/Bre... -

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Basic information

Entry
Database: PDB / ID: 8e6k
Title2H08 Fab in complex with influenza virus neuraminidase from A/Brevig Mission/1/1918 (H1N1)
Components
  • 2H08 fragment antigen binding heavy chain
  • 2H08 fragment antigen binding light chain
  • Neuraminidase
KeywordsVIRAL PROTEIN / influenza / monoclonal antibody / NA / H1N1 / cross-reactive antibody
Function / homology
Function and homology information


: / : / : / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsTurner, H.L. / Ozorowski, G. / Ward, A.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93109C00051 United States
CitationJournal: Immunity / Year: 2023
Title: Human anti-N1 monoclonal antibodies elicited by pandemic H1N1 virus infection broadly inhibit HxN1 viruses in vitro and in vivo.
Authors: Lena Hansen / Meagan McMahon / Hannah L Turner / Xueyong Zhu / Jackson S Turner / Gabriel Ozorowski / Daniel Stadlbauer / Juha Vahokoski / Aaron J Schmitz / Amena A Rizk / Wafaa B Alsoussi / ...Authors: Lena Hansen / Meagan McMahon / Hannah L Turner / Xueyong Zhu / Jackson S Turner / Gabriel Ozorowski / Daniel Stadlbauer / Juha Vahokoski / Aaron J Schmitz / Amena A Rizk / Wafaa B Alsoussi / Shirin Strohmeier / Wenli Yu / José Alberto Choreño-Parra / Luis Jiménez-Alvarez / Alfredo Cruz-Lagunas / Joaquín Zúñiga / Philip A Mudd / Rebecca J Cox / Ian A Wilson / Andrew B Ward / Ali H Ellebedy / Florian Krammer /
Abstract: Neuraminidase (NA) is one of the two influenza virus surface glycoproteins, and antibodies that target it are an independent correlate of protection. However, our current understanding of NA ...Neuraminidase (NA) is one of the two influenza virus surface glycoproteins, and antibodies that target it are an independent correlate of protection. However, our current understanding of NA antigenicity is incomplete. Here, we describe human monoclonal antibodies (mAbs) from a patient with a pandemic H1N1 virus infection in 2009. Two mAbs exhibited broad reactivity and inhibited NA enzyme activity of seasonal H1N1 viruses circulating before and after 2009, as well as viruses with avian or swine N1s. The mAbs provided robust protection from lethal challenge with human H1N1 and avian H5N1 viruses in mice, and both target an epitope on the lateral face of NA. In summary, we identified two broadly protective NA antibodies that share a novel epitope, inhibited NA activity, and provide protection against virus challenge in mice. Our work reaffirms that NA should be included as a target in future broadly protective or universal influenza virus vaccines.
History
DepositionAug 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 9, 2024Group: Data collection / Refinement description / Structure summary
Category: em_3d_fitting_list / em_admin ...em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase
L: 2H08 fragment antigen binding light chain
H: 2H08 fragment antigen binding heavy chain
B: Neuraminidase
I: 2H08 fragment antigen binding light chain
E: 2H08 fragment antigen binding heavy chain
C: Neuraminidase
J: 2H08 fragment antigen binding light chain
F: 2H08 fragment antigen binding heavy chain
D: Neuraminidase
K: 2H08 fragment antigen binding light chain
G: 2H08 fragment antigen binding heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)389,42216
Polymers388,53712
Non-polymers8854
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Neuraminidase


Mass: 49726.387 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Brevig Mission/1/1918(H1N1))
Strain: A/Brevig Mission/1/1918 H1N1 / Gene: NA / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9IGQ6, exo-alpha-sialidase
#2: Antibody
2H08 fragment antigen binding light chain


Mass: 23543.141 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): ExpiCHO / Production host: Homo sapiens (human)
#3: Antibody
2H08 fragment antigen binding heavy chain


Mass: 23864.762 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): ExpiCHO / Production host: Homo sapiens (human)
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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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: 2H08 Fab in complex with influenza virus neuraminidase from A/Brevig Mission/1/1918 (H1N1)
Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Influenza A virus (A/Brevig Mission/1/1918(H1N1))
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris1
2150 mMSodium chlorideNaCl1
312 mMOctyl-beta-glucoside1
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 190000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 700 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 33.5 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 4126

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2EPUimage acquisition
4cryoSPARC3.3.2CTF correctionPatch CTF
9Rosetta2022.11model refinement
10PHENIX1.20.1model refinementreal_space_refine
12cryoSPARC3.3.2final Euler assignment
14cryoSPARC3.3.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45771 / Symmetry type: POINT
Atomic model buildingPDB-ID: 3BEQ

3beq


Accession code: 3BEQ / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00619432
ELECTRON MICROSCOPYf_angle_d1.1126440
ELECTRON MICROSCOPYf_dihedral_angle_d13.316888
ELECTRON MICROSCOPYf_chiral_restr0.0632856
ELECTRON MICROSCOPYf_plane_restr0.0063400

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