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- PDB-8tja: CRYSTAL STRUCTURE OF THE A/Ecuador/1374/2016(H3N2) INFLUENZA VIRU... -

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Basic information

Entry
Database: PDB / ID: 8tja
TitleCRYSTAL STRUCTURE OF THE A/Ecuador/1374/2016(H3N2) INFLUENZA VIRUS HEMAGGLUTININ WITH HUMAN RECEPTOR ANALOG 6'-SLNLN
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / INFLUENZA / HEMAGGLUTININ / RECEPTOR
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / 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
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
DI(HYDROXYETHYL)ETHER / Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsWu, N.C. / Zhu, X. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
Bill & Melinda Gates Foundation United States
CitationJournal: Cell Host Microbe / Year: 2024
Title: Evolution of human H3N2 influenza virus receptor specificity has substantially expanded the receptor-binding domain site.
Authors: Thompson, A.J. / Wu, N.C. / Canales, A. / Kikuchi, C. / Zhu, X. / de Toro, B.F. / Canada, F.J. / Worth, C. / Wang, S. / McBride, R. / Peng, W. / Nycholat, C.M. / Jimenez-Barbero, J. / ...Authors: Thompson, A.J. / Wu, N.C. / Canales, A. / Kikuchi, C. / Zhu, X. / de Toro, B.F. / Canada, F.J. / Worth, C. / Wang, S. / McBride, R. / Peng, W. / Nycholat, C.M. / Jimenez-Barbero, J. / Wilson, I.A. / Paulson, J.C.
History
DepositionJul 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,77026
Polymers55,7852
Non-polymers4,98624
Water8,125451
1
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules

A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules

A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,31178
Polymers167,3546
Non-polymers14,95772
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.687, 100.687, 394.716
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-479-

HOH

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Components

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Hemagglutinin ... , 2 types, 2 molecules AB

#1: Protein Hemagglutinin HA1 chain


Mass: 35788.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Ecuador/1374/2016(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A4P8J8E1
#2: Protein Hemagglutinin HA2 chain


Mass: 19996.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Ecuador/1374/2016(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A3G1NFN9

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Sugars , 4 types, 7 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: 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.: 1
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
#5: 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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1039.937 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-3DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-1-2-3/a4-b1_b3-c1_c4-d1_d6-e2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}}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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
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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Non-polymers , 5 types, 468 molecules

#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.45 Å3/Da / Density % sol: 64.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 50% PEG-200, 0.05 M Lithium sulfate, and 0.1M Tris pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.05→42.94 Å / Num. obs: 49313 / % possible obs: 100 % / Redundancy: 9.4 % / CC1/2: 0.996 / Rpim(I) all: 0.04 / Rsym value: 0.11 / Net I/σ(I): 19.8
Reflection shellResolution: 2.05→2.14 Å / Mean I/σ(I) obs: 2.8 / Num. unique obs: 6056 / CC1/2: 0.859 / Rpim(I) all: 0.3 / Rsym value: 0.83

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→42.94 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2069 2428 4.93 %
Rwork0.1799 --
obs0.1812 49251 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→42.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3849 0 327 451 4627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034242
X-RAY DIFFRACTIONf_angle_d0.5435701
X-RAY DIFFRACTIONf_dihedral_angle_d8.41684
X-RAY DIFFRACTIONf_chiral_restr0.043658
X-RAY DIFFRACTIONf_plane_restr0.003712
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.080.24631420.25392577X-RAY DIFFRACTION95
2.08-2.130.24661400.22292741X-RAY DIFFRACTION100
2.13-2.180.23241540.2142706X-RAY DIFFRACTION100
2.18-2.230.24251250.20692752X-RAY DIFFRACTION100
2.23-2.290.2541450.2122725X-RAY DIFFRACTION100
2.29-2.360.22231400.19932735X-RAY DIFFRACTION100
2.36-2.440.23861400.19892762X-RAY DIFFRACTION100
2.44-2.530.24531410.2132717X-RAY DIFFRACTION100
2.53-2.630.26991310.2042744X-RAY DIFFRACTION100
2.63-2.750.23581560.21162756X-RAY DIFFRACTION100
2.75-2.890.22991430.19632734X-RAY DIFFRACTION100
2.89-3.070.21321390.18492749X-RAY DIFFRACTION99
3.07-3.310.23521470.18422757X-RAY DIFFRACTION100
3.31-3.640.19011280.15612801X-RAY DIFFRACTION100
3.64-4.170.17061370.14772803X-RAY DIFFRACTION100
4.17-5.250.15921490.14082826X-RAY DIFFRACTION100
5.25-42.940.19691710.18912938X-RAY DIFFRACTION100
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)
11.8240.2347-1.70771.24410.81445.9365-0.18020.0244-0.20750.05470.0367-0.00930.8522-0.17340.13720.2432-0.0117-0.01430.2050.06260.315840.7124-43.6225-19.1355
20.5791-0.01740.46570.2365-0.09152.30160.0510.0888-0.098-0.07570.0350.13150.1189-0.3143-0.09390.2478-0.0086-0.04960.25920.01360.31828.0437-36.364-68.0662
31.60550.14910.25872.49070.65272.26470.09530.51590.0709-0.5635-0.05960.0887-0.092-0.2215-0.03330.34170.0434-0.05950.45240.03650.239229.414-28.7338-95.2767
41.2202-0.0602-0.06921.995-0.22030.925-0.00880.27310.0186-0.32460.06820.01040.04650.0273-0.07240.2679-0.015-0.04760.34480.02190.214837.5823-27.8602-89.6843
50.6357-0.06660.35520.5291-0.69312.66830.010.0099-0.0286-0.05390.07180.10290.0054-0.1234-0.08860.17870.0081-0.04940.21730.00950.256829.5643-33.9808-64.2204
60.929-0.25810.67850.32660.48074.09470.01-0.0487-0.0734-0.00070.02530.06380.5097-0.1825-0.03910.2376-0.0442-0.02130.16820.01410.291238.6526-40.2399-38.478
71.9252-0.3467-0.83211.57140.20093.03190.0726-0.16140.03670.1147-0.03740.05310.3314-0.1992-0.02690.2571-0.0668-0.00470.27540.03790.280536.6489-40.9181-10.2096
81.79350.4305-1.59371.753-1.88062.74670.00840.03280.11760.11510.09410.0494-0.1402-0.7083-0.12870.2056-0.00950.00290.28890.02980.304232.5191-32.4707-20.608
92.73690.0922-1.43380.7321-1.12712.3471-0.03320.2579-0.15660.0941-0.05190.0928-0.048-0.34420.11170.2568-0.0365-0.04650.27350.01260.286238.6726-34.0157-60.3346
100.1409-0.0211-0.47160.1657-0.15653.48060.0233-0.0402-0.0370.01120.01040.00820.07380.0016-0.0170.1605-0.02950.00030.19330.00830.253245.3998-33.8777-29.0107
113.30620.8915-0.08593.92370.62212.97460.0182-0.23440.03040.32330.00830.21580.0542-0.3304-0.0180.2467-0.01780.04890.27710.00560.211836.0767-31.5387.3395
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 122 )
3X-RAY DIFFRACTION3chain 'A' and (resid 123 through 201 )
4X-RAY DIFFRACTION4chain 'A' and (resid 202 through 247 )
5X-RAY DIFFRACTION5chain 'A' and (resid 248 through 300 )
6X-RAY DIFFRACTION6chain 'A' and (resid 301 through 325 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 30 )
8X-RAY DIFFRACTION8chain 'B' and (resid 31 through 55 )
9X-RAY DIFFRACTION9chain 'B' and (resid 56 through 75 )
10X-RAY DIFFRACTION10chain 'B' and (resid 76 through 137 )
11X-RAY DIFFRACTION11chain 'B' and (resid 138 through 172 )

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