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- PDB-9c22: Crystal structure of chimeric hemagglutinin cH11/1 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 9c22
TitleCrystal structure of chimeric hemagglutinin cH11/1 in complex with broad protective antibody 3E1
Components
  • (Antibody 3E1 Fab ...) x 2
  • Hemagglutinin
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.6 Å
AuthorsNguyen, T.K.Y. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93109C00051 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structural characterization of influenza group 1 chimeric hemagglutinins as broad vaccine immunogens.
Authors: Yen Thi Kim Nguyen / Xueyong Zhu / Julianna Han / Alesandra J Rodriguez / Weina Sun / Wenli Yu / Peter Palese / Florian Krammer / Andrew B Ward / Ian A Wilson /
Abstract: Chimeric hemagglutinins (cHA) appear to be promising for the design and development of universal influenza vaccines. Influenza A group 1 cHAs, cH5/1, cH8/1, and cH11/1, comprising an H1 stem attached ...Chimeric hemagglutinins (cHA) appear to be promising for the design and development of universal influenza vaccines. Influenza A group 1 cHAs, cH5/1, cH8/1, and cH11/1, comprising an H1 stem attached to either an H5, H8, or H11 globular head, have been used sequentially as vaccine immunogens in human clinical trials and induced high levels of broadly protective antibodies. Using X-ray crystallography and negative-stain electron microscopy, we determined structures of cH5/1, cH8/1, and cH11/1 HAs in their apo (unliganded) and antibody Fab-bound states. Stem-reactive antibodies 3E1 and 31.b.09 recognize their cognate epitopes in cH5/1, cH8/1, and cH11/1 HAs. However, with cH5/1, the head domains are rotated by 35 to 45° around the threefold axis of the HA trimer compared to native HA with a more splayed-open conformation at the stem base. cH11/1 with 3E1 is structurally more native-like but resembles cH5/1 with 31.b.09, whereas cH8/1 with 31.b.09 exhibited a range of closed-to-open stem configurations with some separation of head and stem domains. Furthermore, all of these group 1 cHAs effectively bound a broad head trimer interface antibody and other broad stem antibodies. Thus, the cHAs exhibit structural plasticity without compromising the stem and head trimer interface epitopes for elicitation of influenza A group 1 cross-reactive antibodies.
History
DepositionMay 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: 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.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Hemagglutinin
C: Hemagglutinin
D: Antibody 3E1 Fab light chain
E: Antibody 3E1 Fab heavy chain
H: Hemagglutinin
I: Hemagglutinin
J: Antibody 3E1 Fab light chain
K: Antibody 3E1 Fab heavy chain
L: Hemagglutinin
M: Antibody 3E1 Fab light chain
N: Antibody 3E1 Fab heavy chain
P: Hemagglutinin
Q: Hemagglutinin
R: Antibody 3E1 Fab light chain
S: Antibody 3E1 Fab heavy chain
U: Hemagglutinin
V: Hemagglutinin
W: Antibody 3E1 Fab light chain
X: Antibody 3E1 Fab heavy chain
Y: Hemagglutinin
a: Hemagglutinin
b: Hemagglutinin
c: Antibody 3E1 Fab light chain
d: Antibody 3E1 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)963,88832
Polymers959,88624
Non-polymers4,0038
Water00
1
B: Hemagglutinin
C: Hemagglutinin
D: Antibody 3E1 Fab light chain
E: Antibody 3E1 Fab heavy chain
H: Hemagglutinin
I: Hemagglutinin
J: Antibody 3E1 Fab light chain
K: Antibody 3E1 Fab heavy chain
L: Hemagglutinin
M: Antibody 3E1 Fab light chain
N: Antibody 3E1 Fab heavy chain
Y: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)482,12716
Polymers479,94312
Non-polymers2,1844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
P: Hemagglutinin
Q: Hemagglutinin
R: Antibody 3E1 Fab light chain
S: Antibody 3E1 Fab heavy chain
U: Hemagglutinin
V: Hemagglutinin
W: Antibody 3E1 Fab light chain
X: Antibody 3E1 Fab heavy chain
a: Hemagglutinin
b: Hemagglutinin
c: Antibody 3E1 Fab light chain
d: Antibody 3E1 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)481,76216
Polymers479,94312
Non-polymers1,8194
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)182.433, 194.500, 214.733
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 12 molecules BCHILPQUVYab

#1: Protein
Hemagglutinin


Mass: 56313.016 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper)

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Antibody , 2 types, 12 molecules DJMRWcEKNSXd

#2: Antibody
Antibody 3E1 Fab light chain


Mass: 23483.084 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody
Antibody 3E1 Fab heavy chain


Mass: 23871.846 Da / Num. of mol.: 6
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 , 3 types, 8 molecules

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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}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.: 1 / 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: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 38.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium phosphate dibasic, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 4.6→48.05 Å / Num. obs: 42908 / % possible obs: 99.8 % / Redundancy: 14.4 % / CC1/2: 0.99 / Net I/σ(I): 4.4
Reflection shellResolution: 4.6→4.68 Å / Num. unique obs: 40617 / CC1/2: 0.39

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.6→48.05 Å / SU ML: 0.88 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3247 2037 4.78 %
Rwork0.2926 --
obs0.2941 42653 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.6→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42965 0 265 0 43230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00444263
X-RAY DIFFRACTIONf_angle_d0.74860111
X-RAY DIFFRACTIONf_dihedral_angle_d7.6726084
X-RAY DIFFRACTIONf_chiral_restr0.0496692
X-RAY DIFFRACTIONf_plane_restr0.0067698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.6-4.710.35611450.35042573X-RAY DIFFRACTION96
4.71-4.830.37031530.34152674X-RAY DIFFRACTION100
4.83-4.960.37991420.34932679X-RAY DIFFRACTION100
4.96-5.10.37781310.3432707X-RAY DIFFRACTION100
5.1-5.270.35831240.32942705X-RAY DIFFRACTION100
5.27-5.450.31731260.31732692X-RAY DIFFRACTION100
5.45-5.670.3841180.32452709X-RAY DIFFRACTION99
5.67-5.930.39511300.33222714X-RAY DIFFRACTION100
5.93-6.240.35031290.33412720X-RAY DIFFRACTION100
6.24-6.630.38621650.32212678X-RAY DIFFRACTION100
6.63-7.140.37231430.3252733X-RAY DIFFRACTION100
7.14-7.860.34751410.32212748X-RAY DIFFRACTION100
7.86-8.990.27881070.27362782X-RAY DIFFRACTION100
8.99-11.30.26071250.21392762X-RAY DIFFRACTION99
11.3-48.050.27351580.25352740X-RAY DIFFRACTION95

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