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- PDB-7dea: Structure of an avian influenza H5 hemagglutinin from the influen... -

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Basic information

Entry
Database: PDB / ID: 7dea
TitleStructure of an avian influenza H5 hemagglutinin from the influenza virus A/duck Northern China/22/2017 (H5N6)
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / H5N6 avian influenza virus / Haemagglutinin / Neuraminidase / Acid stability / Human infection
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
Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsSun, H. / Sun, H. / Song, J. / Zhang, W. / Wei, X. / Qi, J. / Gao, G.F. / Liu, J.
CitationJournal: To Be Published
Title: Haemagglutinin and neuraminidase acid stability in H5N6 avian influenza virus confers infection adaptation in mammals
Authors: Sun, H. / Sun, H. / Song, J. / Zhang, W. / Qi, J. / Gao, G.F. / Liu, J.
History
DepositionNov 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 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

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Assembly

Deposited unit
A: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,76215
Polymers168,1616
Non-polymers2,6009
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29580 Å2
ΔGint-110 kcal/mol
Surface area61970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.413, 109.367, 135.913
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hemagglutinin


Mass: 36169.898 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA
Production host: Insect cell expression vector pTIE1 (others)
#2: Protein Hemagglutinin


Mass: 19883.906 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: A0A6M2RI35
#3: 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.: 3
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
#4: 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 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
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: 4.08 Å3/Da / Density % sol: 69.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M TRIS hydrochloride pH 8.5, 2.0 M Ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.7→135.91 Å / Num. obs: 65192 / % possible obs: 99.66 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.166 / Net I/σ(I): 8.4
Reflection shellResolution: 2.7→2.85 Å / Rmerge(I) obs: 0.785 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3762

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NTF

6ntf


Resolution: 2.84→135.91 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.919 / SU B: 0.003 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24603 1988 3.1 %RANDOM
Rwork0.20771 ---
obs0.20889 62976 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.243 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å2-0.05 Å2
2--0.36 Å2-0 Å2
3----0.68 Å2
Refinement stepCycle: 1 / Resolution: 2.84→135.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11799 0 168 13 11980
LS refinement shellResolution: 2.843→2.917 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 148 -
Rwork0.336 4578 -
obs--97.46 %

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