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- PDB-8faq: Structure of Hemagglutinin from Influenza A/Victoria/22/2020 -

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Basic information

Entry
Database: PDB / ID: 8faq
TitleStructure of Hemagglutinin from Influenza A/Victoria/22/2020
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / Influenza A 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 / 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: 2.035 Å
AuthorsHernandez Garcia, A. / Lei, R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R00 AI139445 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)DP2 AT011966 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI167910 United States
CitationJournal: To Be Published
Title: Structure of Hemagglutinin from Influenza A/Victoria/22/2020
Authors: Hernandez Garcia, A. / Lei, R. / Nair, S.K. / Wu, N.
History
DepositionNov 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7226
Polymers55,4131
Non-polymers1,3095
Water2,504139
1
A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,16718
Polymers166,2403
Non-polymers3,92815
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area20240 Å2
ΔGint36 kcal/mol
Surface area56930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.705, 99.705, 395.310
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Hemagglutinin


Mass: 55413.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Victoria/22/2020 / Gene: HA / Cell (production host): sf9 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A6M4ZXR4
#2: 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
#3: 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.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.39 Å3/Da / Density % sol: 63.7 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 50% PEG-200, 0.1M citrate pH 5.5, final pH 6.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12723 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 3, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12723 Å / Relative weight: 1
ReflectionResolution: 2.035→79.252 Å / Num. obs: 48446 / % possible obs: 98.6 % / Redundancy: 20.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.079 / Net I/σ(I): 21.6
Reflection shellResolution: 2.035→2.071 Å / Rmerge(I) obs: 1.642 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2360 / CC1/2: 0.865 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YP4

2yp4


Resolution: 2.035→79.252 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.209 / SU B: 4.229 / SU ML: 0.112 / Average fsc free: 0.8914 / Average fsc work: 0.9087 / Cross valid method: NONE / ESU R: 0.156 / ESU R Free: 0.142 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2291 2400 4.954 %
Rwork0.2028 46046 -
all0.204 --
obs-48446 98.556 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 54.981 Å2
Baniso -1Baniso -2Baniso -3
1--0.005 Å2-0.003 Å2-0 Å2
2---0.005 Å2-0 Å2
3---0.016 Å2
Refinement stepCycle: LAST / Resolution: 2.035→79.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3941 0 0 139 4080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124033
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.6695471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9335486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24722.818220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35615682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2241526
X-RAY DIFFRACTIONr_chiral_restr0.1030.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023068
X-RAY DIFFRACTIONr_nbd_refined0.2150.21675
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22782
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2199
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1870.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.150.218
X-RAY DIFFRACTIONr_mcbond_it3.9015.2471950
X-RAY DIFFRACTIONr_mcangle_it4.9357.8482434
X-RAY DIFFRACTIONr_scbond_it5.0725.672082
X-RAY DIFFRACTIONr_scangle_it6.9688.3363037
X-RAY DIFFRACTIONr_lrange_it8.2971.6485953
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.035-2.0880.3621910.3043310X-RAY DIFFRACTION97.9027
2.088-2.1450.3081870.2743252X-RAY DIFFRACTION98.3977
2.145-2.2080.2731720.2473173X-RAY DIFFRACTION98.2667
2.208-2.2760.2891540.2373113X-RAY DIFFRACTION98.552
2.276-2.350.271410.223010X-RAY DIFFRACTION98.6228
2.35-2.4330.2571570.2082937X-RAY DIFFRACTION98.6922
2.433-2.5240.2681280.2192812X-RAY DIFFRACTION98.8235
2.524-2.6270.2621470.2172730X-RAY DIFFRACTION98.934
2.627-2.7440.2451290.2132592X-RAY DIFFRACTION98.6227
2.744-2.8780.261190.212449X-RAY DIFFRACTION95.6781
2.878-3.0340.261230.2092378X-RAY DIFFRACTION99.1673
3.034-3.2180.2711330.2282272X-RAY DIFFRACTION99.3802
3.218-3.440.2711070.2172140X-RAY DIFFRACTION99.4688
3.44-3.7150.257930.2062025X-RAY DIFFRACTION99.6237
3.715-4.0690.1981200.1861809X-RAY DIFFRACTION99.587
4.069-4.5490.16900.1551702X-RAY DIFFRACTION99.5556
4.549-5.2520.212660.171454X-RAY DIFFRACTION96.5079
5.252-6.4290.211700.1971258X-RAY DIFFRACTION98.4433
6.429-9.0820.203500.1881028X-RAY DIFFRACTION99.9073
9.082-79.2520.141230.236602X-RAY DIFFRACTION98.1162

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