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- PDB-9x5z: B/Phuket/3073/2013-like HA in complex with BP-1A -

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Basic information

Entry
Database: PDB / ID: 9x5z
TitleB/Phuket/3073/2013-like HA in complex with BP-1A
Components
  • (Hemagglutinin ...) x 2
  • BP-1A heavy chain
  • BP-1A light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Hemagglutinin / HA / antibody / influenza B virus / BP-1A / 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 speciesInfluenza B virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsNguyen, V.H.T. / Ma, C.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-IA-113-L02 Taiwan
Ministry of Science and Technology (MoST, Taiwan)NSTC 114-2320-B-001 -018 -MY3 Taiwan
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Broad neutralization of influenza B hemagglutinin antibodies via receptor mimicry and glycan engagement.
Authors: Kuan-Ying A Huang / Hong Thuy Vy Nguyen / Yi-Yin Chen / Kai-Jung Wu / Po-Hsien Hsu / Yo-Min Liu / Tzou-Yien Lin / Che Ma /
Abstract: Influenza B virus contributes to seasonal influenza epidemics and causes global morbidity and mortality. The two antigenically distinct lineages, Victoria and Yamagata, cocirculate within the ...Influenza B virus contributes to seasonal influenza epidemics and causes global morbidity and mortality. The two antigenically distinct lineages, Victoria and Yamagata, cocirculate within the population and are subject to ongoing antigenic drift. In this study, we report the isolation of cross-lineage neutralizing anti-influenza B hemagglutinin (HA) monoclonal antibodies, exhibiting hemagglutination-inhibition activities, from vaccinated adult donors. While some antibodies exhibit reduced activities against recently emerged antigenic variants, BP-1A and BO-6B demonstrate broad neutralization across influenza B viruses isolated over the past two decades and confer protection in mice against lethal challenge from both lineages. Structural analysis of the antibody Fab domains in complex with HA reveals two distinct molecular binding modes: BP-1A uses a long heavy chain CDR3 loop that mimics the ligand to target the receptor-binding site, while BO-6B engages a conserved cleft on the surface of vestigial esterase subdomain through key interactions with glycan moieties. These findings elucidate the molecular basis for broad neutralization by human anti-influenza B HA antibodies and provide insights that may guide the development of immunotherapeutics and rational vaccine design.
History
DepositionOct 14, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin HA1 chain
K: Hemagglutinin HA2 chain
B: Hemagglutinin HA1 chain
M: Hemagglutinin HA2 chain
C: Hemagglutinin HA1 chain
N: Hemagglutinin HA2 chain
H: BP-1A heavy chain
L: BP-1A light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,62426
Polymers272,4238
Non-polymers5,20118
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Hemagglutinin ... , 2 types, 6 molecules ABCKMN

#1: Protein Hemagglutinin HA1 chain


Mass: 39289.141 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus / Strain: B/Phuket/3073/2013-like / Gene: HA / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: A0A4P9HHK4
#2: Protein Hemagglutinin HA2 chain


Mass: 25722.592 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus / Strain: B/Phuket/3073/2013-like / Gene: HA / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: A0A4P9HHK4

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Antibody , 2 types, 2 molecules HL

#3: Antibody BP-1A heavy chain


Mass: 52144.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody BP-1A light chain


Mass: 25243.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Sugars , 2 types, 18 molecules

#5: 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.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#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.: 12 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
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: B/Phuket/3073/2013 HA in complex with BP-1A antibody / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.36 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
11Homo sapiens (human)9606
21Influenza B virus11520B/Phuket/3073/2013
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster) / Cell: ExpiCHO / Plasmid: pcDNA 3.4
Buffer solutionpH: 7.5 / Details: 20 mM Tris, 150 mM NaCl
SpecimenConc.: 2.5 mg/ml / Embedding 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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 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 magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 1.34 sec. / Electron dose: 46.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 12828

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.1particle selection
2EPU3.6.0.6389image acquisition
4cryoSPARC4.5.1CTF correction
7UCSF ChimeraX1.1model fitting
9PHENIX1.14_3260:model refinement
10cryoSPARC4.5.1initial Euler assignment
11cryoSPARC4.5.1final Euler assignment
12cryoSPARC4.5.1classification
13cryoSPARC4.5.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3142850
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 300005 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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