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- PDB-9y41: Crystal structure of hemagglutinin head domain from H1N1 Influenz... -

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Basic information

Entry
Database: PDB / ID: 9y41
TitleCrystal structure of hemagglutinin head domain from H1N1 Influenza A virus A/Victoria/2570/2019 bound to the 49_C09 antibody
Components
  • Antibody 49_C09 heavy chain
  • Antibody 49_C09 light chain
  • Hemagglutinin
KeywordsANTIVIRAL PROTEIN / Hemagglutinin / Head antibody / Influenza / Complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / 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 A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsWang, B. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93021C00015 United States
CitationJournal: Cell Host Microbe / Year: 2026
Title: Childhood immunological imprinting of cross-subtype antibodies targeting the hemagglutinin head domain of influenza viruses.
Authors: Shuk Hang Li / Bo Wang / Gyunghee Jo / Artem Mikelov / Reilly K Atkinson / Valerie Le Sage / Colleen Furey / Jordan T Ort / Naiqing Ye / Sydney Gang / Ruhi Shah / Jefferson J S Santos / ...Authors: Shuk Hang Li / Bo Wang / Gyunghee Jo / Artem Mikelov / Reilly K Atkinson / Valerie Le Sage / Colleen Furey / Jordan T Ort / Naiqing Ye / Sydney Gang / Ruhi Shah / Jefferson J S Santos / Katharina Röltgen / Shilpa A Joshi / Ji-Yeun Lee / Taylor A Pursell / Elizabeth M Drapeau / Julianna Han / Amy P Callear / Ronald G Collman / Arnold S Monto / Emily T Martin / Seema S Lakdawala / Andrew B Ward / Ian A Wilson / Scott D Boyd / Scott E Hensley /
Abstract: Influenza virus cross-subtype antibodies targeting epitopes in the hemagglutinin (HA) head are rare because these epitopes are variable between influenza virus subtypes. We found that a large ...Influenza virus cross-subtype antibodies targeting epitopes in the hemagglutinin (HA) head are rare because these epitopes are variable between influenza virus subtypes. We found that a large proportion of monoclonal antibodies (mAbs) isolated from individuals immunized with the 2021-22 seasonal influenza vaccine bound to an epitope on the HA head of both the H1N1 vaccine strain and H3N2 strains from the mid-1990s. The unmutated common ancestors of many of these mAbs reacted to both the 1990s H3s and the 2021-22 H1 vaccine strain. These cross-subtype antibodies were also found in polyclonal sera, but only among individuals born in the 1990s. Ferrets sequentially exposed to a 1990s H3N2 virus and contemporary influenza vaccine also produced H1/H3 cross-reactive antibodies. Recently, H1N1 viruses have acquired a substitution that abrogates the binding of these antibodies. Together, our study demonstrates how prior influenza virus exposures can influence the specificity of antibodies elicited by entirely different influenza virus subtypes.
History
DepositionSep 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.1May 13, 2026Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 20, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Hemagglutinin
C: Hemagglutinin
H: Antibody 49_C09 heavy chain
L: Antibody 49_C09 light chain
A: Antibody 49_C09 heavy chain
B: Antibody 49_C09 light chain


Theoretical massNumber of molelcules
Total (without water)144,2436
Polymers144,2436
Non-polymers00
Water00
1
G: Hemagglutinin
H: Antibody 49_C09 heavy chain
L: Antibody 49_C09 light chain


Theoretical massNumber of molelcules
Total (without water)72,1223
Polymers72,1223
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Hemagglutinin
A: Antibody 49_C09 heavy chain
B: Antibody 49_C09 light chain


Theoretical massNumber of molelcules
Total (without water)72,1223
Polymers72,1223
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.351, 256.212, 61.773
Angle α, β, γ (deg.)90.00, 99.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hemagglutinin


Mass: 25088.174 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A6M4YP75
#2: Antibody Antibody 49_C09 heavy chain


Mass: 24094.080 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 Antibody 49_C09 light chain


Mass: 22939.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris, pH 8.0, 65% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. obs: 25983 / % possible obs: 87.9 % / Redundancy: 3.9 % / CC1/2: 1 / Rpim(I) all: 0.08 / Rsym value: 0.17 / Net I/σ(I): 9.7
Reflection shellResolution: 2.89→2.95 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1844 / CC1/2: 0.5 / Rpim(I) all: 0.51 / % possible all: 81.5

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Processing

Software
NameVersionClassification
PHENIX1.21refinement
HKL-2000v722data scaling
HKL-2000v722data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→36.66 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2828 2000 7.7 %2000
Rwork0.234 ---
obs0.2378 25979 84.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.89→36.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9937 0 0 0 9937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310210
X-RAY DIFFRACTIONf_angle_d0.58213923
X-RAY DIFFRACTIONf_dihedral_angle_d13.3083651
X-RAY DIFFRACTIONf_chiral_restr0.0451550
X-RAY DIFFRACTIONf_plane_restr0.0121784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.970.4289950.37891137X-RAY DIFFRACTION56
2.97-3.050.35991230.31491473X-RAY DIFFRACTION72
3.05-3.140.35351340.28451611X-RAY DIFFRACTION81
3.14-3.240.36471400.27431673X-RAY DIFFRACTION80
3.24-3.350.32651390.27661668X-RAY DIFFRACTION85
3.35-3.490.34181400.26211688X-RAY DIFFRACTION81
3.49-3.640.28421400.24121675X-RAY DIFFRACTION84
3.64-3.840.29061400.25161676X-RAY DIFFRACTION82
3.84-4.080.26881410.24321693X-RAY DIFFRACTION83
4.08-4.390.271440.21281719X-RAY DIFFRACTION85
4.39-4.830.2571650.19391981X-RAY DIFFRACTION98
4.83-5.530.25231690.21352025X-RAY DIFFRACTION99
5.53-6.960.28881680.23782018X-RAY DIFFRACTION99
6.96-36.660.22421620.1931942X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 26.3458 Å / Origin y: -38.9613 Å / Origin z: 18.9014 Å
111213212223313233
T0.5167 Å20.1087 Å2-0.001 Å2-0.1551 Å20.1632 Å2--0.4632 Å2
L-0.3906 °2-0.2031 °20.0773 °2-0.1914 °2-0.2969 °2---0.5224 °2
S0.058 Å °0.0182 Å °0.0359 Å °-0.165 Å °-0.2017 Å °-0.1521 Å °0.1138 Å °0.0019 Å °-0.5815 Å °
Refinement TLS groupSelection details: all

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