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Basic information

Entry
Database: PDB / ID: 9nja
TitleComputationally optimized broadly reactive influenza B hemagglutinin BC2 bound by antibody #46
Components
  • Fab A Heavy Chain
  • Fab A Light Chain
  • Hemagglutinin
KeywordsVIRAL PROTEIN/Immune System / influenza / antibody / cell entry / hemagglutination / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Function / homology
Function and homology information


viral budding from plasma membrane / host cell surface receptor binding / endocytosis involved in viral entry into host cell / 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
Haemagglutinin, influenzavirus B / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Influenza B virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsDzimianski, J.V. / Kunkel, I. / Balasco Serrao, V.H. / DuBois, R.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00052 United States
CitationJournal: Front Immunol / Year: 2026
Title: Human broadly neutralizing influenza B virus antibodies recognizing hemagglutinin computationally optimized broadly reactive antigens.
Authors: Yailin Campos Mota / John V Dzimianski / Mariana Lopez / Robert A Richardson / Ted M Ross / Ian J A Kunkel / Sara M O'Rourke / Vitor Hugo Balasco Serrão / Rebecca M DuBois / Giuseppe A Sautto /
Abstract: INTRODUCTION: Influenza B viruses (IBVs) are responsible for severe disease and death, similarly to influenza A viruses (IAVs), with a higher number of infections happening in children and the ...INTRODUCTION: Influenza B viruses (IBVs) are responsible for severe disease and death, similarly to influenza A viruses (IAVs), with a higher number of infections happening in children and the elderly. Despite the inclusion of an IBV component in the seasonal influenza vaccine, rates of vaccine effectiveness (VE) are still variable and low in many previous seasons.
METHODS: In this work, longitudinal profiling of IBV hemagglutinin (HA)-specific B-cell responses was described following influenza vaccination in 15 vaccinated participants over four consecutive ...METHODS: In this work, longitudinal profiling of IBV hemagglutinin (HA)-specific B-cell responses was described following influenza vaccination in 15 vaccinated participants over four consecutive influenza seasons. These individuals belonged to different age groups and monoclonal antibodies (mAbs) showing broad binding and functional antibody profiles were isolated from the plasmablasts of one individual.
RESULTS: These individuals possessed different breadths and magnitudes of antibody responses to a panel of IBV historical and more recent vaccine strains. In particular, young adults (age 23-33) ...RESULTS: These individuals possessed different breadths and magnitudes of antibody responses to a panel of IBV historical and more recent vaccine strains. In particular, young adults (age 23-33) showed a higher magnitude and breadth of antibody response compared to middle-aged (age 55-58) and elderly (age 65-77) participants who instead showed a lower albeit detectable antibody response. Interestingly, one of the isolated mAbs, mAb #46, had the broadest response with a broad binding and potent functional activity against historical and recent IBV strains spanning both Victoria and Yamagata lineages and including binding to IBV computationally optimized broadly reactive antigen (COBRA) HAs. Importantly, mAb #46 administration, either therapeutically or prophylactically, fully protected IBV-challenged mice. Structural characterization of the mAb #46-HA complex by cryo-electron microscopy single-particle analysis revealed that mAb #46 targets a conserved epitope within the HA receptor binding site.
DISCUSSION: This study highlights the presence of broadly neutralizing antibodies in the human repertoire that may be recalled by vaccination with COBRA HA, although this hypothesis will be confirmed ...DISCUSSION: This study highlights the presence of broadly neutralizing antibodies in the human repertoire that may be recalled by vaccination with COBRA HA, although this hypothesis will be confirmed in upcoming clinical trials.
History
DepositionFeb 27, 2025Deposition site: RCSB / Processing site: RCSB
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab A Light Chain
H: Fab A Heavy Chain
A: Hemagglutinin
K: Fab A Light Chain
J: Fab A Heavy Chain
B: Hemagglutinin
P: Fab A Light Chain
Q: Fab A Heavy Chain
C: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,88418
Polymers316,2849
Non-polymers2,6009
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "B"
d_2ens_1chain "A"
d_3ens_1chain "C"
d_1ens_2chain "Q"
d_2ens_2chain "J"
d_3ens_2chain "H"
d_1ens_3chain "K"
d_2ens_3chain "L"
d_3ens_3chain "P"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1PROPROPROPROBF36 - 32236 - 322
d_12ens_1NAGNAGNAGNAGEK1
d_13ens_1NAGNAGNAGNAGEK2
d_14ens_1NAGNAGNAGNAGBO601
d_15ens_1NAGNAGNAGNAGBP602
d_21ens_1PROPROPROPROAC36 - 32236 - 322
d_22ens_1NAGNAGNAGNAGDJ1
d_23ens_1NAGNAGNAGNAGDJ2
d_24ens_1NAGNAGNAGNAGAM601
d_25ens_1NAGNAGNAGNAGAN602
d_31ens_1PROPROPROPROCI36 - 32236 - 322
d_32ens_1NAGNAGNAGNAGFL1
d_33ens_1NAGNAGNAGNAGFL2
d_34ens_1NAGNAGNAGNAGCQ601
d_35ens_1NAGNAGNAGNAGCR602
d_11ens_2VALVALVALVALQH2 - 1112 - 124
d_21ens_2VALVALVALVALJE2 - 1112 - 124
d_31ens_2VALVALVALVALHB2 - 1112 - 124
d_11ens_3GLUGLUVALVALKD9 - 1119 - 111
d_21ens_3GLUGLUVALVALLA9 - 1119 - 111
d_31ens_3GLUGLUVALVALPG9 - 1119 - 111

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.500152763904, -0.865937186867, -3.40562266895E-5), (0.865937186574, -0.500152764816, 2.74777779931E-5), (-4.08273457147E-5, -1.57474665157E-5, 0.999999999043)390.271818855, 104.601251428, 0.00957941352624
2given(-0.500008250797, 0.866020640086, 8.97595395425E-6), (-0.866020639776, -0.500008250862, 2.34878001375E-5), (2.48289707457E-5, 3.97073247574E-6, 0.999999999684)104.567233159, 390.251413851, -0.00554500610664
3given(-0.50000794287, -0.8660208175, 2.68972615752E-5), (0.866020817858, -0.50000794296, 3.74544223028E-6), (1.02052134893E-5, 2.51663393322E-5, 0.999999999631)390.24989434, 104.571521082, -0.00507727661397
4given(-0.499838053735, 0.866118881827, -5.07975151331E-5), (-0.866118883155, -0.499838051646, 4.86760091699E-5), (1.67686796414E-5, 6.83268087612E-5, 0.999999997525)104.534583434, 390.231320908, -0.0130618853308
5given(-0.500150637041, -0.865938415416, -3.12158236249E-5), (0.865938415057, -0.500150637846, 2.81039084123E-5), (-3.99488680144E-5, -1.29747931387E-5, 0.999999999118)390.271174585, 104.600682011, 0.00905794255908
6given(-0.500010966269, 0.866019072288, 6.61237241446E-6), (-0.866019071908, -0.500010966255, 2.67682557571E-5), (2.64880787378E-5, 7.65798080499E-6, 0.99999999962)104.568258446, 390.250996143, -0.00629443801918

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Components

#1: Antibody Fab A Light Chain


Mass: 23206.629 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab A Heavy Chain


Mass: 24845.973 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Hemagglutinin


Mass: 57375.242 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus / Gene: HA / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P17504
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 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.: 6 / 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: Complex of a viral protein with two antibodies / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 35025

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.3particle selection
2SerialEM4.1.21image acquisition
4cryoSPARC4.5.3CTF correction
7UCSF ChimeraXmodel fitting
8Cootmodel fitting
10cryoSPARC4.5.3initial Euler assignment
11cryoSPARC4.5.3final Euler assignment
12cryoSPARC4.5.3classification
13cryoSPARC4.5.33D reconstruction
14PHENIX1.21.2_5419model refinement
15ISOLDEmodel refinement
16Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1165223
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 209227 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model building

3D fitting-ID: 1 / Accession code: 9NJ3

IDPDB-IDPdb chain-IDChain-IDInitial refinement model-IDSource nameType
19NJ3

9nj3

AA1PDBexperimental model
2H2AlphaFoldin silico model
3L2AlphaFoldin silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 69.34 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002211946
ELECTRON MICROSCOPYf_angle_d0.452916197
ELECTRON MICROSCOPYf_chiral_restr0.04331821
ELECTRON MICROSCOPYf_plane_restr0.00422088
ELECTRON MICROSCOPYf_dihedral_angle_d9.50314557
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2FBELECTRON MICROSCOPYNCS constraints1.63741827793E-11
ens_1d_3FBELECTRON MICROSCOPYNCS constraints3.49500069082E-13
ens_2d_2HQELECTRON MICROSCOPYNCS constraints1.26059578785E-12
ens_2d_3HQELECTRON MICROSCOPYNCS constraints3.33496760512E-11
ens_3d_2DKELECTRON MICROSCOPYNCS constraints2.93392996105E-13
ens_3d_3DKELECTRON MICROSCOPYNCS constraints3.75670424386E-13

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