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- PDB-8x2d: Crystal structure of H5 hemagglutinin from swan-infecting H5N8 in... -

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Basic information

Entry
Database: PDB / ID: 8x2d
TitleCrystal structure of H5 hemagglutinin from swan-infecting H5N8 influenza virus complexed with avian receptor analog LSTc
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
6'-sialyl-N-acetyllactosamine / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 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. / Miao, 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

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,47414
Polymers173,1123
Non-polymers4,36211
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18030 Å2
ΔGint0 kcal/mol
Surface area62330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.680, 107.034, 134.326
Angle α, β, γ (deg.)90.000, 100.470, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein / Non-polymers , 2 types, 278 molecules ABC

#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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 11 molecules

#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 836.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-3DGalpb1-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_b4-c1_c6-d2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}LINUCSPDB-CARE
#3: 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
#4: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 674.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6'-sialyl-N-acetyllactosamine
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b6-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#5: 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.: 6 / 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

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Details

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: 3.29 Å3/Da / Density % sol: 62.67 %
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: 2.48→50 Å / Num. obs: 78715 / % possible obs: 100 % / Redundancy: 5.6 % / Biso Wilson estimate: 50.22 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 12.917
Reflection shellResolution: 2.48→2.59 Å / Rmerge(I) obs: 0.838 / Num. unique obs: 7802

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→49.63 Å / SU ML: 0.3392 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.2763
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2524 2000 2.55 %
Rwork0.2342 76551 -
obs0.2346 78551 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.79 Å2
Refinement stepCycle: LAST / Resolution: 2.48→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11763 0 289 275 12327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010712319
X-RAY DIFFRACTIONf_angle_d1.125516690
X-RAY DIFFRACTIONf_chiral_restr0.06211843
X-RAY DIFFRACTIONf_plane_restr0.00922152
X-RAY DIFFRACTIONf_dihedral_angle_d5.70171706
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.550.35441280.34314906X-RAY DIFFRACTION89.83
2.55-2.620.37111430.3335461X-RAY DIFFRACTION99.88
2.62-2.690.36111440.32755509X-RAY DIFFRACTION99.67
2.69-2.780.34841420.31385455X-RAY DIFFRACTION99.73
2.78-2.880.29611440.29525497X-RAY DIFFRACTION99.81
2.88-2.990.28871440.2895495X-RAY DIFFRACTION99.82
2.99-3.130.30411440.26535502X-RAY DIFFRACTION99.81
3.13-3.290.27371420.25695456X-RAY DIFFRACTION99.98
3.29-3.50.25631450.25455541X-RAY DIFFRACTION99.86
3.5-3.770.24361420.22595480X-RAY DIFFRACTION99.98
3.77-4.150.23661450.21035527X-RAY DIFFRACTION99.96
4.15-4.750.19631450.18555550X-RAY DIFFRACTION99.95
4.75-5.980.22461450.19575548X-RAY DIFFRACTION99.93
5.98-49.630.231470.2115624X-RAY DIFFRACTION99.65
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.39034107906-0.2480512115552.997727345140.340434984842-0.493969869119.8839457259-0.349498275022-0.212248366870.2321610943580.513820946997-0.0575384250462-0.248894093893-1.13894031515-0.1954360863310.3896537091350.8019597670640.00100101675226-0.1874505201580.362698604623-0.03131083447520.54013883051670.116837940272.652844920439.7235495042
21.61670722833-0.2999850374540.4027719963192.610537434140.0255788725612.846248876860.02396620144090.08127847411470.1623082846890.101491316013-0.168649261937-0.21185176382-0.3900457119760.1700055293220.1345889192320.376994812739-0.0104476388190.008951142875170.1997316491260.02194295183350.35103470301863.418713565368.93339722285.83502717079
32.388096489030.9413119945693.564856172921.327017237761.955045331537.631932090810.0290809991538-0.1403725281980.0104912790450.516328896810.0786134410211-0.4353368672220.0956150278190.616952778011-0.1265139207640.882411272499-0.0029694128411-0.2319836193110.5887238491010.01162058257330.62479121490585.566015053162.019549426565.790402056
42.17022325671-0.06468177410325.144149698390.249954022440.04044185456529.038318004180.599197578809-0.770611483011-0.3992631074080.560580351718-0.11733372096-0.07910335769171.32220948888-1.12587484106-0.4692570756591.12491264014-0.298113484771-0.1470497305550.8276702075860.1051407963150.55299156076955.73118365834.307763771845.7260120237
52.447492455270.5882466829041.139855113132.18210253685-0.5772086603573.415853334490.286235142547-0.540124145241-0.0243818261510.308962163312-0.1961027349370.2022553260260.259791432947-0.40050093133-0.07708246366940.39650991943-0.122821366215-0.008360324887860.361687540754-0.01777177000080.4063019782442.371107426742.32502046214.5188710877
60.618877843745-0.0303582533331.268961424960.162713665968-0.9687647984769.06724389408-0.0158012556363-0.2341296351010.02348436553520.554107330716-0.158929800644-0.1313901241660.08234995328960.0703368474780.1310159823491.28636846514-0.13469184802-0.280320651110.5254380399370.07388407355450.64151179829973.965056414443.008692692570.7643008199
71.49454919853-0.1466107243051.627337931890.8423736368870.5212501681264.703602623610.2451515566450.234331030071-0.3457686923480.325302848160.188597087081-0.4151052628930.7932878143621.48474215552-0.4182619302480.5577285361980.0989936890093-0.1601499127330.792680557443-0.06894835579270.7771861216993.316658911439.738660427330.0158073247
82.37477268289-0.2109471033641.317072977711.611003733260.2920328301733.146741683420.29161737460.279198717075-0.4506427142640.001616874299580.0522451190159-0.4594773305690.8449820541640.633827825202-0.2786363231430.4632338803110.144473845333-0.04196863854110.38323898052-0.1012555567610.576970131773.987660007235.87331932221.21212807235
91.627168976340.4692273531660.8293632194030.622697609684-0.5213141863163.494715412430.357025874744-0.371798922981-0.5766676864540.6767560460190.190223172081-0.5479564959330.8486124621871.17534431815-0.5617663517871.092626497840.29943811192-0.3748219190440.978960247166-0.06844109404670.87294222598499.527257220641.576234147257.9290907586
106.30637497369-3.285081053567.302284661213.02963938058-4.158500100787.915842088940.388221211104-0.504099868555-0.4739835565720.01560035488010.049883357651-0.2220634034911.40804872252-0.148042587145-0.5141522322950.7493177068060.0595687309269-0.1176459460410.5547838200220.03228526706280.65906569650485.102140545844.217950626148.4590380777
113.1815509443-0.4455180070183.153792254990.426301424984-1.224637197394.813213649990.103003562209-0.955764613601-0.9609060377591.827216083590.835556584622-0.9768054893451.436525891431.40268753877-0.9197731948492.054372963540.418040733786-0.6941818065451.865589172540.06428961037931.3348403334104.81542701738.55665004690.2610797326
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 92 )AA1 - 921 - 92
22chain 'A' and (resid 93 through 285 )AA93 - 28593 - 285
33chain 'A' and (resid 286 through 500 )AA286 - 500286 - 490
44chain 'B' and (resid 1 through 92 )BB1 - 921 - 92
55chain 'B' and (resid 93 through 285 )BB93 - 28593 - 285
66chain 'B' and (resid 286 through 500 )BB286 - 500286 - 500
77chain 'C' and (resid 1 through 92 )CC1 - 921 - 92
88chain 'C' and (resid 93 through 285 )CC93 - 28593 - 285
99chain 'C' and (resid 286 through 366 )CC286 - 366286 - 366
1010chain 'C' and (resid 367 through 451 )CC367 - 451367 - 451
1111chain 'C' and (resid 452 through 500 )CC452 - 500452 - 500

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