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- PDB-8tj9: CRYSTAL STRUCTURE OF THE A/Michigan/15/2014(H3N2) INFLUENZA VIRUS... -

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Basic information

Entry
Database: PDB / ID: 8tj9
TitleCRYSTAL STRUCTURE OF THE A/Michigan/15/2014(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 / TRIETHYLENE GLYCOL / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)60,61621
Polymers55,9202
Non-polymers4,69619
Water8,395466
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)181,84963
Polymers167,7596
Non-polymers14,08957
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area54710 Å2
ΔGint-95 kcal/mol
Surface area59410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.591, 100.591, 394.890
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: 35923.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Michigan/15/2014(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0Y0S9M3
#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/Michigan/15/2014(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0Y0S9M3

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Sugars , 3 types, 7 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.: 3
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 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
#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.: 3
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 , 6 types, 478 molecules

#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 3.44 Å3/Da / Density % sol: 64.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 40% PEG-400, 0.2 M Lithium sulfate, and 0.1M Tris pH 8.5

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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: Apr 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.9→42.53 Å / Num. obs: 61131 / % possible obs: 99.9 % / Redundancy: 18.8 % / CC1/2: 0.999 / Rpim(I) all: 0.02 / Rsym value: 0.09 / Net I/σ(I): 42.3
Reflection shellResolution: 1.9→1.96 Å / Mean I/σ(I) obs: 3 / Num. unique obs: 5474 / CC1/2: 0.925 / Rpim(I) all: 0.23 / Rsym value: 0.99

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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: 1.9→42.53 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1854 3135 5.13 %
Rwork0.1606 --
obs0.1619 61121 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→42.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3870 0 306 466 4642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094246
X-RAY DIFFRACTIONf_angle_d0.9955725
X-RAY DIFFRACTIONf_dihedral_angle_d9.51671
X-RAY DIFFRACTIONf_chiral_restr0.066662
X-RAY DIFFRACTIONf_plane_restr0.009715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.25321510.22772609X-RAY DIFFRACTION100
1.93-1.960.19971520.18932565X-RAY DIFFRACTION100
1.96-20.21821370.17722623X-RAY DIFFRACTION100
2-2.030.20911350.17182585X-RAY DIFFRACTION100
2.03-2.070.22621460.17522610X-RAY DIFFRACTION100
2.07-2.110.19371460.17292614X-RAY DIFFRACTION100
2.11-2.160.21251530.16742587X-RAY DIFFRACTION100
2.16-2.210.21941400.16272609X-RAY DIFFRACTION100
2.21-2.260.22371360.15722608X-RAY DIFFRACTION100
2.26-2.330.23751320.16912652X-RAY DIFFRACTION100
2.33-2.390.181300.15752627X-RAY DIFFRACTION100
2.39-2.470.23081300.16382624X-RAY DIFFRACTION100
2.47-2.560.18291670.16962597X-RAY DIFFRACTION100
2.56-2.660.20971280.16622656X-RAY DIFFRACTION100
2.66-2.780.19991550.17742604X-RAY DIFFRACTION100
2.78-2.930.18861530.16752637X-RAY DIFFRACTION100
2.93-3.110.16411450.15792633X-RAY DIFFRACTION100
3.11-3.350.19571640.16572649X-RAY DIFFRACTION100
3.35-3.690.15981180.14952681X-RAY DIFFRACTION100
3.69-4.230.14881250.1372690X-RAY DIFFRACTION100
4.23-5.320.15971490.13582711X-RAY DIFFRACTION100
5.32-42.530.18791430.17922815X-RAY DIFFRACTION99
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)
10.95770.2448-0.42241.25850.42641.96670.00260.1192-0.1870.0689-0.13590.16470.5175-0.47680.09680.2147-0.0186-0.06230.1668-0.00760.2829-58.001513.379419.1753
20.54420.20630.25320.2413-0.60252.90440.0174-0.033-0.1074-0.14940.08980.0360.448-0.1475-0.11560.2682-0.0318-0.06470.15620.00480.2849-54.93998.415538.1053
30.5787-0.28420.15830.73320.0692.57290.0333-0.2558-0.32040.21510.06180.02830.55380.214-0.09370.35840.039-0.09940.27720.08340.3218-42.492.452671.0843
41.215-0.0556-0.02891.11150.06711.4856-0.0546-0.5744-0.12520.51170.1519-0.08610.24780.1026-0.12230.50710.0894-0.10660.50610.08480.2586-40.800510.058390.0157
51.5110.53480.70763.1171-1.25771.1055-0.0811-0.5780.09670.80880.15630.0341-0.2426-0.0583-0.1220.64120.0677-0.0570.5039-0.03420.272-39.277424.251693.704
61.5719-0.27030.32481.2188-0.01181.4048-0.0437-0.5981-0.13610.43440.08430.03790.0403-0.0512-0.06270.48680.0286-0.06370.41770.0560.2278-44.930616.027390.0047
70.64740.02690.57920.43010.24791.82520.0743-0.1109-0.0450.26560.0791-0.12480.11110.1745-0.15940.34310.0283-0.09960.33260.07280.2879-40.20039.829176.0368
81.57090.0742-0.26181.6186-0.4531.92780.1117-0.1086-0.23650.02560.0819-0.11360.43150.0335-0.19990.26490.028-0.0740.19250.02960.2923-48.52877.308751.9221
90.94430.05890.18450.4449-0.14394.0380.0712-0.0899-0.0910.0030.01190.02530.5312-0.3823-0.02070.1678-0.0395-0.02580.10680.01940.2192-54.196313.385438.4744
101.1507-0.1609-0.54210.5396-0.0971.45380.02570.1695-0.0128-0.18390.0447-0.07530.417-0.198-0.06160.2863-0.0177-0.05170.131-0.02980.2535-53.587311.229110.2171
110.40560.13710.75971.42832.62328.93420.05560.0059-0.04350.04260.0108-0.0820.55270.2918-0.11080.21290.0416-0.05130.1437-0.01310.2598-44.386511.993620.7288
120.4923-0.56110.32941.69811.06132.1388-0.0207-0.159-0.17490.22630.10460.01630.280.214-0.07670.2697-0.0193-0.05490.23850.05730.2651-48.780216.467660.5444
130.2653-0.0102-0.09850.21880.43952.61340.04890.0034-0.0407-0.01950.02760.0139-0.0638-0.0673-0.07030.15630.0029-0.00750.10730.00240.2322-51.596822.700630.9259
141.50870.2002-0.56052.0662-0.05241.5171-0.01890.2496-0.1766-0.28410.041-0.07150.16040.0636-0.03350.27220.01050.0030.217-0.05340.2226-46.708715.871-6.5975
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 49 )
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 89 )
4X-RAY DIFFRACTION4chain 'A' and (resid 90 through 195 )
5X-RAY DIFFRACTION5chain 'A' and (resid 196 through 214 )
6X-RAY DIFFRACTION6chain 'A' and (resid 215 through 247 )
7X-RAY DIFFRACTION7chain 'A' and (resid 248 through 275 )
8X-RAY DIFFRACTION8chain 'A' and (resid 276 through 300 )
9X-RAY DIFFRACTION9chain 'A' and (resid 301 through 325 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 30 )
11X-RAY DIFFRACTION11chain 'B' and (resid 31 through 55 )
12X-RAY DIFFRACTION12chain 'B' and (resid 56 through 75 )
13X-RAY DIFFRACTION13chain 'B' and (resid 76 through 132 )
14X-RAY DIFFRACTION14chain 'B' and (resid 133 through 173 )

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