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- PDB-9nrb: Crystal structure of H5 hemagglutinin Q226L mutant from the influ... -

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Basic information

Entry
Database: PDB / ID: 9nrb
TitleCrystal structure of H5 hemagglutinin Q226L mutant from the influenza virus A/duck/France/1611008h/16 with LSTc
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / H1N1 / Antibody / Hemagglutinin
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
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsLin, T.H. / Zhu, Y. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93021C00015 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: The Q226L mutation can convert a highly pathogenic H5 2.3.4.4e virus to bind human-type receptors.
Authors: Rios Carrasco, M. / Lin, T.H. / Zhu, X. / Gabarroca Garcia, A. / Uslu, E. / Liang, R. / Spruit, C.M. / Richard, M. / Boons, G.J. / Wilson, I.A. / de Vries, R.P.
History
DepositionMar 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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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
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,52217
Polymers172,1746
Non-polymers4,34811
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34930 Å2
ΔGint-119 kcal/mol
Surface area63440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.915, 176.398, 226.377
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Hemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin HA1 chain


Mass: 36976.926 Da / Num. of mol.: 3 / Mutation: Q226L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/duck/France/161108h/2016(H5N8) / Gene: HA
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: A0A6M2RJB8
#2: Protein Hemagglutinin HA2 chain


Mass: 20414.504 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/duck/France/161108h/2016(H5N8) / Gene: HA
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: A0A6M2RJB8

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Sugars , 4 types, 11 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 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 N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-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
DNeup5Aca2-3DGalpb1-3DGlcpNAcb1-3DGalpb1-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_b3-c1_c3-d2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(3+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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: isolated from a natural 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, 62 molecules

#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris, 2M ammonium sulfate, 0.2M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.65→26.81 Å / Num. obs: 110745 / % possible obs: 99.6 % / Redundancy: 11.4 % / CC1/2: 0.99 / Rpim(I) all: 0.085 / Rrim(I) all: 0.29 / Net I/σ(I): 10.8
Reflection shellResolution: 2.65→2.7 Å / Num. unique obs: 10532 / CC1/2: 0.39 / Rpim(I) all: 0.85 / Rrim(I) all: 2.9

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→26.81 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 5538 5 %
Rwork0.2093 --
obs0.2107 110720 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→26.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11825 0 286 62 12173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212382
X-RAY DIFFRACTIONf_angle_d0.55516776
X-RAY DIFFRACTIONf_dihedral_angle_d17.6494922
X-RAY DIFFRACTIONf_chiral_restr0.0441859
X-RAY DIFFRACTIONf_plane_restr0.0042162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.680.38311560.4052997X-RAY DIFFRACTION86
2.68-2.710.41272080.37263484X-RAY DIFFRACTION100
2.71-2.750.34431880.33423495X-RAY DIFFRACTION100
2.75-2.780.31641700.29223473X-RAY DIFFRACTION100
2.78-2.820.31341870.28733502X-RAY DIFFRACTION100
2.82-2.860.31711670.28483519X-RAY DIFFRACTION100
2.86-2.90.31541860.28393518X-RAY DIFFRACTION100
2.9-2.940.35811910.27723469X-RAY DIFFRACTION100
2.94-2.990.30891850.28173502X-RAY DIFFRACTION100
2.99-3.040.31231740.28123515X-RAY DIFFRACTION100
3.04-3.090.30212110.26833500X-RAY DIFFRACTION100
3.09-3.140.28611750.24043461X-RAY DIFFRACTION100
3.14-3.20.26611880.23443527X-RAY DIFFRACTION100
3.2-3.270.26472000.23193467X-RAY DIFFRACTION100
3.27-3.340.24911750.22633540X-RAY DIFFRACTION100
3.34-3.420.28171820.22413532X-RAY DIFFRACTION100
3.42-3.50.26031800.22223481X-RAY DIFFRACTION100
3.5-3.60.24561790.21163565X-RAY DIFFRACTION100
3.6-3.70.26321950.21073476X-RAY DIFFRACTION99
3.7-3.820.24021720.1983533X-RAY DIFFRACTION100
3.82-3.960.20241800.18113520X-RAY DIFFRACTION100
3.96-4.120.20462020.17743533X-RAY DIFFRACTION100
4.12-4.30.18121810.16773543X-RAY DIFFRACTION100
4.3-4.530.18431760.15923540X-RAY DIFFRACTION100
4.53-4.810.2011890.16133524X-RAY DIFFRACTION99
4.81-5.180.20681820.17243547X-RAY DIFFRACTION100
5.18-5.70.20191970.17263585X-RAY DIFFRACTION100
5.7-6.510.18981840.19353603X-RAY DIFFRACTION100
6.51-8.160.22821740.22023636X-RAY DIFFRACTION99
8.17-26.810.23522040.21163595X-RAY DIFFRACTION95

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