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- PDB-8x26: Crystal structure of H5 hemagglutinin from human-infecting H5N8 i... -

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Basic information

Entry
Database: PDB / ID: 8x26
TitleCrystal structure of H5 hemagglutinin from human-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
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å
AuthorsJin, X.Y. / Song, H. / Han, P. / Qi, J.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82122040 China
CitationJournal: To Be Published
Title: Enhanced binding of Sialyl Lewis X to hemagglutinin contributes to H5N8 mammalian pathogenicity and infectivity
Authors: Jin, X. / Han, P. / Zhang, C. / Maio, A.D. / Shi, Y. / Qi, J. / Bi, Y. / Liu, Y. / Song, H. / Gao, G.F.
History
DepositionNov 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)353,52720
Polymers346,1286
Non-polymers7,40014
Water00
1
A: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,08611
Polymers173,0643
Non-polymers4,0238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18070 Å2
ΔGint-1 kcal/mol
Surface area62500 Å2
MethodPISA
2
B: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,4419
Polymers173,0643
Non-polymers3,3776
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17430 Å2
ΔGint-7 kcal/mol
Surface area62700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.978, 263.809, 131.624
Angle α, β, γ (deg.)90.000, 101.641, 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: 57687.926 Da / Num. of mol.: 6
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: 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.: 3
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
#3: Polysaccharide
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 836.744 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGlcpNAcb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-1-3/a3-b1_b3-c1_c3-d2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}LINUCSPDB-CARE
#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.: 5 / Source method: obtained synthetically / 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
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: 3.59 Å3/Da / Density % sol: 65.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 3 % dextran sulfate sodium salt, 0.1 M bicine pH 7.7, 18 % 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: Nov 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 86324 / % possible obs: 99.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 78.51 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 8.8
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 1.372 / Num. unique obs: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.12→48.279 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.884 / SU B: 0.006 / SU ML: 0 / Cross valid method: FREE R-VALUE / ESU R: 0.48 / ESU R Free: 0.49
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2705 1835 2.34 %
Rwork0.265 76579 -
all0.265 --
obs-78414 90.833 %
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: 107.287 Å2
Baniso -1Baniso -2Baniso -3
1-2.354 Å20 Å22.935 Å2
2--0.806 Å2-0 Å2
3----4.027 Å2
Refinement stepCycle: LAST / Resolution: 3.12→48.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23282 0 496 0 23778
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
3.12-3.2010.391790.3836810.3863540.9030.89359.17530.346
3.201-3.2880.4071310.3648220.36161690.8830.90580.28850.321
3.288-3.3830.3211170.34249230.34260210.930.91583.7070.306
3.383-3.4870.3661060.3349460.33158620.9150.92286.18220.292
3.487-3.60.2911260.30749820.30756660.9380.93590.15180.272
3.6-3.7260.3281290.28849230.28954750.9240.94392.2740.257
3.726-3.8660.2971150.2848510.28153260.9430.94793.24070.25
3.866-4.0230.2921130.26647110.26650700.9470.95395.14790.234
4.023-4.20.2351140.25246010.25148780.960.95896.65850.223
4.2-4.4040.2631050.24145170.24246970.9510.96198.40320.216
4.404-4.640.241040.2342750.23144440.9630.96598.53740.207
4.64-4.9180.2481010.2340780.2342180.9630.96699.07540.21
4.918-5.2540.242850.23738670.23739930.9670.96298.97320.217
5.254-5.6690.232890.23935670.23836880.9670.96499.13230.22
5.669-6.2020.251720.25632730.25633780.9610.95899.02310.234
6.202-6.920.288730.25529930.25630810.950.9699.51310.237
6.92-7.9630.243650.23926700.2427440.9520.96399.6720.232
7.963-9.6870.231500.20722640.20823180.9660.97399.82740.209
9.687-13.4310.201390.19717910.19718300.9760.9761000.21
13.431-48.2790.23220.4678440.4610890.960.88179.52250.428

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