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- PDB-8tjb: CRYSTAL STRUCTURE OF THE A/Texas/73/2017(H3N2) INFLUENZA VIRUS HE... -

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Basic information

Entry
Database: PDB / ID: 8tjb
TitleCRYSTAL STRUCTURE OF THE A/Texas/73/2017(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: 2.45 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)60,4239
Polymers56,1082
Non-polymers4,3157
Water2,702150
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)181,26927
Polymers168,3246
Non-polymers12,94521
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 area49090 Å2
ΔGint59 kcal/mol
Surface area61860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.240, 100.240, 391.849
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-218-

HOH

21B-265-

HOH

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Components

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Hemagglutinin ... , 2 types, 2 molecules AB

#1: Protein Hemagglutinin HA1 chain


Mass: 35981.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Texas/73/2017(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A1W6AW68
#2: Protein Hemagglutinin HA2 chain


Mass: 20126.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Texas/73/2017(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A1W6AW68

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Sugars , 5 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.: 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 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
#5: 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.: 2
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
#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-(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
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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, 150 molecules

#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 3.38 Å3/Da / Density % sol: 63.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 30% 1,2-propanediol, 20% PEG-400, and 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.03317 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.45→43.14 Å / Num. obs: 28518 / % possible obs: 99.9 % / Redundancy: 9.1 % / CC1/2: 0.998 / Rpim(I) all: 0.04 / Rsym value: 0.1 / Net I/σ(I): 30
Reflection shellResolution: 2.45→2.55 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3105 / CC1/2: 0.867 / Rpim(I) all: 0.41 / Rsym value: 1

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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: 2.45→43.14 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2773 1483 5.21 %
Rwork0.2384 --
obs0.2424 28464 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→43.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3875 0 288 150 4313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034245
X-RAY DIFFRACTIONf_angle_d0.6075745
X-RAY DIFFRACTIONf_dihedral_angle_d11.53693
X-RAY DIFFRACTIONf_chiral_restr0.046687
X-RAY DIFFRACTIONf_plane_restr0.003716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.530.36551220.35342395X-RAY DIFFRACTION100
2.53-2.620.411480.32892401X-RAY DIFFRACTION100
2.62-2.720.33881460.32592406X-RAY DIFFRACTION100
2.72-2.850.36891420.30352425X-RAY DIFFRACTION100
2.85-30.35991120.27992444X-RAY DIFFRACTION99
3-3.180.29361280.26332420X-RAY DIFFRACTION100
3.18-3.430.28291160.24792462X-RAY DIFFRACTION100
3.43-3.770.24671690.21722424X-RAY DIFFRACTION100
3.77-4.320.25211170.20332491X-RAY DIFFRACTION100
4.32-5.440.24551400.20632503X-RAY DIFFRACTION100
5.44-43.140.26881430.23632610X-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)
11.4541-0.02190.1940.64280.07231.3657-0.0824-0.1778-0.38560.3323-0.16170.0440.7756-0.06440.26590.5723-0.0850.09790.44510.08710.545740.2721-43.2997-18.8751
21.07410.4452-0.45291.34850.43031.75130.02030.1809-0.2762-0.29030.11010.46470.4424-1.0317-0.07280.2943-0.0171-0.07150.44450.01190.512726.1559-37.8233-61.824
32.52490.1594-0.32480.82020.10561.21250.06140.83880.01-0.53050.09710.49380.1243-0.6075-0.07660.5322-0.01-0.20230.76860.0470.571528.9652-31.4922-82.5246
41.17480.39860.36142.57520.85041.7576-0.54210.8170.3197-0.82570.40541.1750.435-1.14910.1840.7785-0.1133-0.25220.9836-0.03460.608922.6119-37.6978-91.2128
52.33780.53420.41491.9579-0.90861.5494-0.07591.07690.1209-1.28020.03950.2755-0.3939-0.26460.10750.8370.0116-0.15821.00620.04430.503432.6735-26.8195-96.4599
62.92250.08460.14071.334-0.54692.0969-0.04010.48980.0402-0.42590.0618-0.25480.20280.10630.07340.6982-0.0098-0.09650.72180.00430.416937.2692-27.9652-89.4074
70.99560.0886-0.07150.46910.30591.6678-0.05380.0741-0.0583-0.16950.10640.19460.0244-0.5191-0.07140.4185-0.0257-0.09590.5490.01730.491629.9997-34.0552-62.3997
80.8332-0.7858-0.50720.92130.14895.8244-0.0294-0.2728-0.26230.0751-0.04030.02411.16320.38230.10010.4683-0.03640.04210.35040.02810.453239.9659-43.0146-30.9577
91.5383-0.0518-0.4191.0213-0.08290.7458-0.0052-0.7562-0.25910.2763-0.06290.25970.3859-0.2684-0.0670.5149-0.01610.07860.64090.09810.435137.7653-40.2382-13.2528
100.77290.0258-0.31431.1066-0.32871.9388-0.1137-0.1251-0.13160.28940.07060.087-0.3107-0.87750.08790.41720.00580.07550.56030.02710.553431.8438-33.6498-15.7784
110.8398-0.19790.21910.8805-0.58050.2524-0.0156-0.39020.6335-0.03590.0860.2254-0.61340.16340.20650.4215-0.0461-0.0090.6744-0.10380.707233.4734-28.3594-52.2031
121.1784-0.0308-1.55030.9043-0.85353.0252-0.02920.0586-0.1435-0.0556-0.00340.06320.322-0.2510.09440.1965-0.0509-0.01120.24250.01630.371945.1515-34.4788-40.0726
131.51630.5403-0.3491.4695-0.03981.12210.1152-0.39720.00510.4526-0.03030.1693-0.037-0.0654-0.13850.75110.01750.11740.89670.02380.507237.2421-31.74936.0912
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 132 )
4X-RAY DIFFRACTION4chain 'A' and (resid 133 through 153 )
5X-RAY DIFFRACTION5chain 'A' and (resid 154 through 201 )
6X-RAY DIFFRACTION6chain 'A' and (resid 202 through 247 )
7X-RAY DIFFRACTION7chain 'A' and (resid 248 through 308 )
8X-RAY DIFFRACTION8chain 'A' and (resid 309 through 325 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 25 )
10X-RAY DIFFRACTION10chain 'B' and (resid 26 through 55 )
11X-RAY DIFFRACTION11chain 'B' and (resid 56 through 65 )
12X-RAY DIFFRACTION12chain 'B' and (resid 66 through 126 )
13X-RAY DIFFRACTION13chain 'B' and (resid 127 through 172 )

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