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- PDB-9y40: Crystal structure of hemagglutinin head domain from H3N2 Influenz... -

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Basic information

Entry
Database: PDB / ID: 9y40
TitleCrystal structure of hemagglutinin head domain from H3N2 Influenza A virus A/New York/631/1996 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: 3.71 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
A: Hemagglutinin
H: Antibody 49_C09 heavy chain
L: Antibody 49_C09 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2014
Polymers76,9803
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-27 kcal/mol
Surface area29730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.358, 170.358, 95.831
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Hemagglutinin


Mass: 29946.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/New York/631/1996(H3N2))
Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q1PT16
#2: Antibody Antibody 49_C09 heavy chain


Mass: 24094.080 Da / Num. of mol.: 1
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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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.: 1
Source method: isolated from a genetically manipulated source
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
Has ligand of interestY
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: 5.21 Å3/Da / Density % sol: 76.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 4M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 16731 / % possible obs: 100 % / Redundancy: 18.2 % / CC1/2: 1 / Rpim(I) all: 0.07 / Rsym value: 0.28 / Net I/σ(I): 7
Reflection shellResolution: 3.7→3.76 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1600 / CC1/2: 0.92 / Rpim(I) all: 0.19 / Rsym value: 0.73

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Processing

Software
NameVersionClassification
PHENIX1.21refinement
PDB_EXTRACTdata extraction
HKL-2000v722data reduction
HKL-2000v722data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.71→45.57 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 23.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 1657 9.89 %1653
Rwork0.2027 ---
obs0.2063 16728 96.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.71→45.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5348 0 0 0 5348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025492
X-RAY DIFFRACTIONf_angle_d0.5417491
X-RAY DIFFRACTIONf_dihedral_angle_d11.0751992
X-RAY DIFFRACTIONf_chiral_restr0.044843
X-RAY DIFFRACTIONf_plane_restr0.005961
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.71-3.810.34831240.26571179X-RAY DIFFRACTION92
3.82-3.940.3111350.23961210X-RAY DIFFRACTION95
3.94-4.080.27711340.22371233X-RAY DIFFRACTION95
4.08-4.240.2571320.2091230X-RAY DIFFRACTION97
4.24-4.430.23581420.21011257X-RAY DIFFRACTION98
4.44-4.670.23341410.17461260X-RAY DIFFRACTION98
4.67-4.960.21381380.16961264X-RAY DIFFRACTION98
4.96-5.340.2241390.18861277X-RAY DIFFRACTION98
5.34-5.880.22861440.20261278X-RAY DIFFRACTION98
5.88-6.730.2251430.21471276X-RAY DIFFRACTION98
6.73-8.460.24411400.20281295X-RAY DIFFRACTION98
8.47-45.570.19991450.19171334X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 91.3853 Å / Origin y: -37.5576 Å / Origin z: 16.1086 Å
111213212223313233
T0.4878 Å2-0.0429 Å2-0.0342 Å2-0.5117 Å2-0.0329 Å2--0.4956 Å2
L1.1447 °2-1.0304 °2-0.2442 °2-1.8691 °20.5081 °2--1.2992 °2
S-0.0397 Å °-0.1821 Å °0.0198 Å °-0.0644 Å °0.0613 Å °0.0704 Å °-0.1071 Å °0.0711 Å °0.0014 Å °
Refinement TLS groupSelection details: all

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