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- PDB-9nr2: Crystal structure of H5 hemagglutinin from the influenza virus A/... -

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Basic information

Entry
Database: PDB / ID: 9nr2
TitleCrystal structure of H5 hemagglutinin from the influenza virus A/black swan/Akita/1/2016 with LSTa
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: 2.71 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 13, 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
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,06513
Polymers170,9016
Non-polymers2,1647
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34130 Å2
ΔGint-152 kcal/mol
Surface area60620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.241, 100.397, 132.067
Angle α, β, γ (deg.)90.00, 125.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Hemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin HA1


Mass: 36524.426 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: A0A1L7N0F8
#2: Protein Hemagglutinin HA2


Mass: 20442.520 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: A0A1L7N0F8

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Sugars , 3 types, 7 molecules

#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}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: 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.: 5 / Source method: obtained synthetically / 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, 17 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.94 Å3/Da / Density % sol: 58.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M sodium iodide, 20% PEG 3350

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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: 2.71→35.65 Å / Num. obs: 52384 / % possible obs: 97.7 % / Redundancy: 6.2 % / CC1/2: 0.98 / Rpim(I) all: 0.1 / Rrim(I) all: 0.24 / Net I/σ(I): 13.2
Reflection shellResolution: 2.71→2.76 Å / Num. unique obs: 5206 / CC1/2: 0.63 / Rpim(I) all: 0.63 / Rrim(I) all: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→35.65 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.272 2644 5.05 %
Rwork0.2233 --
obs0.2258 52313 97.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.71→35.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11911 0 141 17 12069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212326
X-RAY DIFFRACTIONf_angle_d0.48616697
X-RAY DIFFRACTIONf_dihedral_angle_d9.3421831
X-RAY DIFFRACTIONf_chiral_restr0.0411807
X-RAY DIFFRACTIONf_plane_restr0.0032177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.760.4441390.34622537X-RAY DIFFRACTION96
2.76-2.820.35861440.33172656X-RAY DIFFRACTION99
2.82-2.870.37661550.29672635X-RAY DIFFRACTION99
2.87-2.940.36351500.28252649X-RAY DIFFRACTION99
2.94-30.35221410.27792654X-RAY DIFFRACTION99
3-3.080.33691190.27012634X-RAY DIFFRACTION99
3.08-3.160.34171650.26162617X-RAY DIFFRACTION98
3.16-3.260.37571390.27182564X-RAY DIFFRACTION96
3.26-3.360.34571240.27062618X-RAY DIFFRACTION98
3.36-3.480.33261350.26142655X-RAY DIFFRACTION100
3.48-3.620.29631460.22382702X-RAY DIFFRACTION100
3.62-3.780.30751370.23972537X-RAY DIFFRACTION95
3.78-3.980.24031280.21612615X-RAY DIFFRACTION97
3.98-4.230.24551600.18862631X-RAY DIFFRACTION99
4.23-4.560.22241400.17712610X-RAY DIFFRACTION97
4.56-5.020.22781410.17742442X-RAY DIFFRACTION91
5.02-5.740.23691280.18592658X-RAY DIFFRACTION98
5.74-7.220.22881300.22112674X-RAY DIFFRACTION98
7.22-35.650.2151230.20662581X-RAY DIFFRACTION93

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