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- PDB-8x29: Crystal structure of H5 hemagglutinin from swan-infecting H5N8 in... -

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Basic information

Entry
Database: PDB / ID: 8x29
TitleCrystal structure of H5 hemagglutinin from swan-infecting H5N8 influenza virus in complex with LSTa
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM 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
beta-D-galactopyranose / N-acetyl-alpha-neuraminic acid / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.613 Å
AuthorsJin, X.Y. / Han, P. / Song, H. / Qi, J.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82122040 China
CitationJournal: EMBO Rep / Year: 2026
Title: Hemagglutinin double-mutation enhances binding of human-infecting avian influenza virus clade 2.3.4.4b H5Ny to human and SLe receptors.
Authors: Xiyue Jin / Pu Han / Yuxuan Wang / Haichen Wang / Chunge Zhang / Antonio Di Maio / Jin Yu / Tianjiao Hao / Yuhang Gu / Zeyu Zhang / Wei Zhang / Jianxun Qi / Yuhai Bi / Xu Zhang / Lei Sun / ...Authors: Xiyue Jin / Pu Han / Yuxuan Wang / Haichen Wang / Chunge Zhang / Antonio Di Maio / Jin Yu / Tianjiao Hao / Yuhang Gu / Zeyu Zhang / Wei Zhang / Jianxun Qi / Yuhai Bi / Xu Zhang / Lei Sun / Ningli Wang / Yan Liu / Hao Song / George F Gao /
Abstract: Clade 2.3.4.4b H5Ny highly pathogenic avian influenza viruses (HPAIVs) continue to circulate worldwide, posing zoonotic threats, especially with recent cattle outbreaks. The mechanisms by which these ...Clade 2.3.4.4b H5Ny highly pathogenic avian influenza viruses (HPAIVs) continue to circulate worldwide, posing zoonotic threats, especially with recent cattle outbreaks. The mechanisms by which these viruses adapt to mammalian hosts while maintaining a broad avian tropism remain poorly understood. Here, we demonstrate that two naturally occurring mutations (K222Q and S227R) in the hemagglutinin (HA) of a human-infecting H5N8 strain, first identified in 2020, enhance binding affinity for both α2-6-linked and Sialyl Lewis (SLe) glycans, which may underlie the broad tissue binding and cross-species potential. Structural analyses reveal that these mutations expand receptor specificity for these glycans, which are abundant in the human respiratory tract and duck trachea, providing a possible molecular basis for cross-species transmission. Our findings suggest that clade 2.3.4.4b H5Ny viruses evolved dual receptor specificity as early as the 2020 Russian H5N8 strain, potentially contributing to sporadic human infections and widespread dissemination among birds and mammals.
History
DepositionNov 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _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
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,25617
Polymers173,1123
Non-polymers3,14414
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.151, 108.495, 133.192
Angle α, β, γ (deg.)90.000, 99.789, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Hemagglutinin


Mass: 57703.988 Da / Num. of mol.: 3 / Mutation: A86V, T188I, H273N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Baculovirus transfer vector pFASTBAC1 / References: UniProt: A0A8E4ZAK5
#2: 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: isolated from a genetically manipulated source
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
#3: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.3 Å3/Da / Density % sol: 62.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 3 % dextran sulfate sodium salt, 0.1 M bicine pH 8.5, 19 % (w/v) PEG20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 66519 / % possible obs: 98.1 % / Redundancy: 4.3 % / Biso Wilson estimate: 36.48 Å2 / Rmerge(I) obs: 0.167 / Net I/σ(I): 9.291
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 1.074 / Num. unique obs: 6680

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.613→26.328 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.162 / SU B: 11.207 / SU ML: 0.224 / Average fsc free: 0.9557 / Average fsc work: 0.9723 / Cross valid method: FREE R-VALUE / ESU R: 0.511 / ESU R Free: 0.281
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2306 1903 3.01 %
Rwork0.1841 61310 -
all0.186 --
obs-63213 92.658 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 36.264 Å2
Baniso -1Baniso -2Baniso -3
1-1.859 Å20 Å2-2.837 Å2
2--0.938 Å2-0 Å2
3----1.715 Å2
Refinement stepCycle: LAST / Resolution: 2.613→26.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11784 0 200 401 12385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01212254
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611280
X-RAY DIFFRACTIONr_angle_refined_deg1.8261.82416602
X-RAY DIFFRACTIONr_angle_other_deg0.6261.77126034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.34851467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.297557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.527102076
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.76210612
X-RAY DIFFRACTIONr_chiral_restr0.0830.21804
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214468
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022842
X-RAY DIFFRACTIONr_nbd_refined0.2230.22283
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.210426
X-RAY DIFFRACTIONr_nbtor_refined0.1870.25843
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.26582
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.2430
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1020.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1810.27
X-RAY DIFFRACTIONr_nbd_other0.2010.225
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1570.23
X-RAY DIFFRACTIONr_mcbond_it3.5643.4635886
X-RAY DIFFRACTIONr_mcbond_other3.5643.4635886
X-RAY DIFFRACTIONr_mcangle_it5.6736.2097347
X-RAY DIFFRACTIONr_mcangle_other5.6736.2117348
X-RAY DIFFRACTIONr_scbond_it4.7194.046368
X-RAY DIFFRACTIONr_scbond_other4.7194.046367
X-RAY DIFFRACTIONr_scangle_it7.6277.1569255
X-RAY DIFFRACTIONr_scangle_other7.6267.1569256
X-RAY DIFFRACTIONr_lrange_it10.01932.26413239
X-RAY DIFFRACTIONr_lrange_other10.0132.28513178
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.613-2.680.3621240.29237410.29449860.8960.93777.51710.225
2.68-2.7530.381180.29141090.29448450.9060.94187.24460.237
2.753-2.8320.2751300.24540620.24646920.950.95989.34360.194
2.832-2.9180.2571210.22840200.22945970.9470.96490.08050.182
2.918-3.0120.2951250.24439590.24644600.9360.96291.56950.207
3.012-3.1160.2941230.23438960.23643030.9440.96593.40.198
3.116-3.2320.261180.20337960.20441390.9570.97494.56390.174
3.232-3.3620.2391110.18636910.18840110.9660.9894.78930.167
3.362-3.5090.2421120.1935990.19138600.9660.97896.13990.175
3.509-3.6770.2391090.16934610.17136810.9650.98496.98450.158
3.677-3.8720.2331030.17333090.17535060.9630.98397.31890.16
3.872-4.1010.191950.14531280.14633120.9770.98797.31280.138
4.101-4.3770.182930.14429510.14531380.9760.98897.00450.137
4.377-4.7170.181860.12527780.12629490.9810.99197.11770.124
4.717-5.150.18780.1425050.14126690.9820.98996.77780.14
5.15-5.7310.178730.14323340.14424820.9840.9996.97820.145
5.731-6.5660.184640.14620300.14721710.9810.98996.45320.142
6.566-7.9190.198540.15817600.15918880.9780.98696.08050.157
7.919-10.7250.174430.15813830.15914880.9870.98895.83330.167
10.725-26.3280.226230.2767980.2759710.9790.95884.5520.281

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