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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: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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