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- PDB-8ez7: Structure of 1F04 Fab in complex with A/Moscow/10/1999 (H3N2) inf... -

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Basic information

Entry
Database: PDB / ID: 8ez7
TitleStructure of 1F04 Fab in complex with A/Moscow/10/1999 (H3N2) influenza virus neuraminidase
Components
  • Heavy chain of influenza virus neuraminidase antibody 1F04
  • Light chain of influenza virus neuraminidase antibody 1F04
  • Neuraminidase
KeywordsHydrolase/Immune System / antibody / neuraminidase / influenza / Hydrolase-Immune System complex
Function / homology
Function and homology information


exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / 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
alpha-D-mannopyranose / Neuraminidase
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsMou, Z. / Lei, R. / Wu, N.C. / Dai, X.
Funding support4items
OrganizationGrant numberCountry
Other governmentR01 AI167910
Other governmentDP2 AT011966
Other privateMichelson Prizes for Human Immunology and Vaccine Research
Other privateSearle Scholars Program
CitationJournal: Immunity / Year: 2023
Title: Leveraging vaccination-induced protective antibodies to define conserved epitopes on influenza N2 neuraminidase.
Authors: Ruipeng Lei / Wooseob Kim / Huibin Lv / Zongjun Mou / Michael J Scherm / Aaron J Schmitz / Jackson S Turner / Timothy J C Tan / Yiquan Wang / Wenhao O Ouyang / Weiwen Liang / Joel Rivera- ...Authors: Ruipeng Lei / Wooseob Kim / Huibin Lv / Zongjun Mou / Michael J Scherm / Aaron J Schmitz / Jackson S Turner / Timothy J C Tan / Yiquan Wang / Wenhao O Ouyang / Weiwen Liang / Joel Rivera-Cardona / Chuyun Teo / Claire S Graham / Christopher B Brooke / Rachel M Presti / Chris K P Mok / Florian Krammer / Xinghong Dai / Ali H Ellebedy / Nicholas C Wu /
Abstract: There is growing appreciation for neuraminidase (NA) as an influenza vaccine target; however, its antigenicity remains poorly characterized. In this study, we isolated three broadly reactive N2 ...There is growing appreciation for neuraminidase (NA) as an influenza vaccine target; however, its antigenicity remains poorly characterized. In this study, we isolated three broadly reactive N2 antibodies from the plasmablasts of a single vaccinee, including one that cross-reacts with NAs from seasonal H3N2 strains spanning five decades. Although these three antibodies have diverse germline usages, they recognize similar epitopes that are distant from the NA active site and instead involve the highly conserved underside of NA head domain. We also showed that all three antibodies confer prophylactic and therapeutic protection in vivo, due to both Fc effector functions and NA inhibition through steric hindrance. Additionally, the contribution of Fc effector functions to protection in vivo inversely correlates with viral growth inhibition activity in vitro. Overall, our findings advance the understanding of NA antibody response and provide important insights into the development of a broadly protective influenza vaccine.
History
DepositionOct 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Heavy chain of influenza virus neuraminidase antibody 1F04
L: Light chain of influenza virus neuraminidase antibody 1F04
A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3278
Polymers68,5723
Non-polymers1,7555
Water00
1


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

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Components

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Protein , 1 types, 1 molecules A

#3: Protein Neuraminidase


Mass: 42767.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Moscow/10/1999(H3N2))
Cell line (production host): Sf9 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8AZ87, exo-alpha-sialidase

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Antibody , 2 types, 2 molecules HL

#1: Antibody Heavy chain of influenza virus neuraminidase antibody 1F04


Mass: 13984.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): expi293F / Production host: Homo sapiens (human)
#2: Antibody Light chain of influenza virus neuraminidase antibody 1F04


Mass: 11820.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): expi293F / Production host: Homo sapiens (human)

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Sugars , 3 types, 5 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: 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.: 3 / 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

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Details

Has ligand of interestY

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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: Structure of 1F04 Fab in complex with A/Moscow/10/1999 (H3N2) influenza virus neuraminidase
Type: COMPLEX
Details: Structure of 1F04 Fab in complex with A/Moscow/10/1999 (H3N2) influenza virus neuraminidase
Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Influenza A virus
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen 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 defocus max: 1500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20_4459: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 480812 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035038
ELECTRON MICROSCOPYf_angle_d0.5166836
ELECTRON MICROSCOPYf_dihedral_angle_d9.719753
ELECTRON MICROSCOPYf_chiral_restr0.043760
ELECTRON MICROSCOPYf_plane_restr0.004876

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