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- PDB-8tj8: CRYSTAL STRUCTURE OF THE A/Moscow/10/1999(H3N2) INFLUENZA VIRUS H... -

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Basic information

Entry
Database: PDB / ID: 8tj8
TitleCRYSTAL STRUCTURE OF THE A/Moscow/10/1999(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
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)59,49410
Polymers56,0132
Non-polymers3,4818
Water93752
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)178,48230
Polymers168,0386
Non-polymers10,44424
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
Buried area45140 Å2
ΔGint19 kcal/mol
Surface area60800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.031, 100.031, 385.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Hemagglutinin ... , 2 types, 2 molecules AB

#1: Protein Hemagglutinin HA1 chain


Mass: 35912.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Moscow/10/1999(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: I6SI59
#2: Protein Hemagglutinin HA2 chain


Mass: 20100.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Moscow/10/1999(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: I6SI59

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Sugars , 5 types, 8 molecules

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


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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.: 1
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
#6: 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: obtained synthetically
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
#7: 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.: 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 , 1 types, 52 molecules

#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.31 Å3/Da / Density % sol: 62.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 40% PEG-400 and 0.2 M Calcium acetate, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.55→43.04 Å / Num. obs: 24519 / % possible obs: 100 % / Redundancy: 9.2 % / CC1/2: 0.998 / Rpim(I) all: 0.04 / Rsym value: 0.11 / Net I/σ(I): 17.9
Reflection shellResolution: 2.55→2.64 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2399 / CC1/2: 0.904 / Rpim(I) all: 0.33 / Rsym value: 0.97

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→43.04 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 29.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2576 1228 5.02 %
Rwork0.2095 --
obs0.217 24477 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.56→43.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3866 0 230 52 4148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044178
X-RAY DIFFRACTIONf_angle_d0.7035657
X-RAY DIFFRACTIONf_dihedral_angle_d6.835650
X-RAY DIFFRACTIONf_chiral_restr0.046663
X-RAY DIFFRACTIONf_plane_restr0.008716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.660.47311350.39642511X-RAY DIFFRACTION99
2.66-2.780.38751280.31672541X-RAY DIFFRACTION100
2.78-2.930.35991330.26242553X-RAY DIFFRACTION100
2.93-3.110.32341210.2692566X-RAY DIFFRACTION100
3.11-3.350.27771450.25942556X-RAY DIFFRACTION100
3.35-3.690.26821380.20492575X-RAY DIFFRACTION100
3.69-4.220.2411410.19532587X-RAY DIFFRACTION100
4.22-5.320.20041310.16332623X-RAY DIFFRACTION100
5.32-43.040.24281560.19412737X-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)
11.01580.7547-1.18780.7531-0.06543.44230.031-0.3039-0.47330.57220.1227-0.02451.0271-0.4071-0.33170.7785-0.1016-0.06070.59810.1260.579740.1887-43.2115-19.395
20.783-0.10371.07510.3264-0.15451.85510.09920.0675-0.1683-0.0610.01760.14960.1469-0.308-0.01230.4558-0.0087-0.05060.5520.07440.541725.6004-36.1138-62.4738
31.2083-0.0068-0.12281.31891.43662.50710.25730.2502-0.144-0.2599-0.17450.1133-0.0485-0.2881-0.05360.6091-0.0206-0.0950.55490.06130.570929.8248-32.7464-78.5665
42.2992-0.46310.0891.09110.82462.72770.14390.73480.1749-0.16360.30410.27920.1561-0.6605-0.42410.78810.0468-0.15921.1190.08040.712321.5558-29.9704-94.8007
52.4372-0.5624-0.00851.8203-0.34821.44920.16490.84780.2496-0.6853-0.03740.1181-0.2175-0.2877-0.07970.89760.0766-0.09810.96570.12030.615328.0499-21.8582-94.6489
61.28970.059-0.60961.3984-0.22761.87980.030.6291-0.0289-0.7063-0.0706-0.1733-0.22330.29170.00090.79540.0056-0.02470.91910.0380.59837.1127-26.7828-95.2422
73.117-1.4158-0.47472.9623-0.24493.22450.60420.462-0.55990.3758-0.127-0.48881.0791.1206-0.60370.91930.1549-0.12191.0803-0.20560.722536.8341-41.413-94.449
81.49040.116-0.06491.1553-0.34672.36150.0280.26870.24590.2216-0.0829-0.4244-0.1688-0.06920.07890.7544-0.0359-0.03930.68710.08660.545835.7168-21.3556-88.1296
91.60350.54030.75781.4952-1.28682.11530.0530.3869-0.0013-0.0479-0.13960.1913-0.37710.2046-0.01520.61030.0302-0.07610.70070.03440.535229.0519-25.3833-77.561
100.5908-0.0971.1747-0.12720.77383.19250.2069-0.0357-0.11090.0421-0.0270.16750.2837-0.2353-0.22470.4409-0.0285-0.0620.42720.07230.549232.9541-38.8507-46.9581
111.64810.001-0.09781.12930.86632.7720.0291-0.5846-0.15430.53520.06390.19510.2989-0.741-0.07450.5288-0.05550.02060.71120.11440.523934.4832-36.7846-15.0955
121.5264-0.91320.44321.5768-0.91410.6381-0.3275-0.1373-0.26710.07970.13870.4061-0.3366-0.50440.34490.62270.057-0.04030.71760.0320.623935.8554-31.0145-56.7201
132.14780.0954-4.09892.9147-1.50579.05060.1456-0.2846-0.4017-0.77680.7442.20211.11430.0567-0.91031.0137-0.0859-0.10570.56040.08650.811345.7818-41.3769-73.719
140.4187-0.0693-0.05340.4799-0.49162.977-0.0199-0.1343-0.15150.0488-0.0645-0.0041-0.0914-0.1140.05550.3465-0.0214-0.00670.40730.03380.524845.1563-33.3039-35.1678
150.9999-0.03660.56041.3997-0.29941.8470.008-0.3174-0.29870.39190.17460.385-0.2595-0.8408-0.25410.76890.01780.1061.00730.10970.601936.0336-33.19062.7159
163.56290.7096-0.64232.4870.53022.4118-0.1112-1.1029-0.01351.24680.33670.4891-0.2932-0.572-0.29520.8779-0.09490.15540.95770.00630.505640.8993-30.340312.7966
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 89 )
3X-RAY DIFFRACTION3chain 'A' and (resid 90 through 122 )
4X-RAY DIFFRACTION4chain 'A' and (resid 123 through 146 )
5X-RAY DIFFRACTION5chain 'A' and (resid 147 through 175 )
6X-RAY DIFFRACTION6chain 'A' and (resid 176 through 213 )
7X-RAY DIFFRACTION7chain 'A' and (resid 214 through 228 )
8X-RAY DIFFRACTION8chain 'A' and (resid 229 through 249 )
9X-RAY DIFFRACTION9chain 'A' and (resid 250 through 269 )
10X-RAY DIFFRACTION10chain 'A' and (resid 270 through 325 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 55 )
12X-RAY DIFFRACTION12chain 'B' and (resid 56 through 70 )
13X-RAY DIFFRACTION13chain 'B' and (resid 71 through 75 )
14X-RAY DIFFRACTION14chain 'B' and (resid 76 through 126 )
15X-RAY DIFFRACTION15chain 'B' and (resid 127 through 158 )
16X-RAY DIFFRACTION16chain 'B' and (resid 159 through 173 )

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