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- PDB-9mqw: Crystal structure of influenza virus N2 neuraminidase from A/Sing... -

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Basic information

Entry
Database: PDB / ID: 9mqw
TitleCrystal structure of influenza virus N2 neuraminidase from A/Singapore/INFIMH-16-0019/2016 (H3N2)
ComponentsNeuraminidase
KeywordsVIRAL PROTEIN/HYDROLASE / HYDROLASE / IMMUNE SYSTEM / Influenza virus / neuraminidase / neutralization / substrate mimicry / VIRAL PROTEIN / VIRAL PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsZhu, X. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00051 United States
CitationJournal: Biorxiv / Year: 2025
Title: Structure and function of a cross-neutralizing influenza neuraminidase antibody that accommodates recent N2 NA Asn245 glycosylation.
Authors: Zhu, X. / Khalil, A.M. / Piepenbrink, M.S. / Yu, W. / Ma, Y. / Martinez-Sobrido, L. / Wilson, I.A. / Kobie, J.J.
History
DepositionJan 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,10719
Polymers43,5321
Non-polymers4,57518
Water2,936163
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,42676
Polymers174,1264
Non-polymers18,30072
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area40310 Å2
ΔGint-589 kcal/mol
Surface area52260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.320, 137.320, 155.516
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-727-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Neuraminidase


Mass: 43531.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: NA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A5B8WQ58, exo-alpha-sialidase

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Sugars , 3 types, 6 molecules

#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.: 4
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: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}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.: 1 / Source method: obtained synthetically / 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

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Non-polymers , 3 types, 175 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 4.21 Å3/Da / Density % sol: 70.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M citric acid, pH 4.0, 2.4 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.29→48.55 Å / Num. obs: 32018 / % possible obs: 95.4 % / Redundancy: 17.6 % / CC1/2: 0.993 / Rpim(I) all: 0.06 / Rsym value: 0.26 / Net I/σ(I): 12.6
Reflection shellResolution: 2.29→2.34 Å / Num. unique obs: 1258 / CC1/2: 0.629 / Rpim(I) all: 0.63 / Rsym value: 1

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5127: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→48.55 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2143 1597 5.02 %
Rwork0.1748 --
obs0.1768 31802 94.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.29→48.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2996 0 287 163 3446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053338
X-RAY DIFFRACTIONf_angle_d0.8314533
X-RAY DIFFRACTIONf_dihedral_angle_d15.9311102
X-RAY DIFFRACTIONf_chiral_restr0.052539
X-RAY DIFFRACTIONf_plane_restr0.005551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.360.34621070.33911901X-RAY DIFFRACTION66
2.36-2.450.36291190.31412385X-RAY DIFFRACTION83
2.45-2.540.39711470.29092589X-RAY DIFFRACTION90
2.54-2.660.26961290.25072768X-RAY DIFFRACTION96
2.66-2.80.30211530.22192864X-RAY DIFFRACTION99
2.8-2.970.23631470.20142898X-RAY DIFFRACTION100
2.97-3.20.23151610.19412895X-RAY DIFFRACTION100
3.2-3.530.21241610.15282900X-RAY DIFFRACTION100
3.53-4.040.15641340.13122961X-RAY DIFFRACTION100
4.04-5.080.15231650.11362948X-RAY DIFFRACTION100
5.09-48.550.1981740.17263096X-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)
11.360.0989-0.54481.046-0.75970.751-0.04410.0175-0.0261-0.0076-0.04740.09-0.0163-0.00130.07590.2685-0.0305-0.02150.2413-0.0280.3487-13.7986-11.6364-51.6395
20.9593-0.2465-0.76991.6843-0.47541.3614-0.0578-0.0089-0.2168-0.0468-0.02030.12330.04050.03450.06580.2545-0.01-0.0070.27070.01370.3587-6.4745-19.4193-46.3574
31.5913-0.5809-0.65631.90840.42413.33480.0725-0.0370.00050.0671-0.08890.29510.3371-0.22040.04420.3228-0.05020.02920.32420.01580.4525-16.1894-29.6026-44.286
43.0008-0.9727-0.38762.0195-1.10861.6494-0.0244-0.0459-0.62760.04560.15950.45140.2609-0.3744-0.10120.3424-0.07410.04960.32510.01140.5434-21.8899-27.318-39.3925
51.4546-0.3075-0.12951.5638-0.64671.911-0.06410.1477-0.2259-0.1799-0.1380.23340.3285-0.21470.20.3741-0.0630.01080.346-0.06060.5583-32.5415-27.5073-48.9532
62.0635-0.3631-0.66991.5754-0.4432.06930.0040.0534-0.15040.0230.09320.29420.1089-0.1773-0.09230.2585-0.0359-0.00430.2777-0.02920.411-32.0481-13.4566-49.5003
72.8949-1.7209-1.67082.28771.56033.8050.07230.4051-0.005-0.2621-0.130.1639-0.0592-0.140.03430.2107-0.0618-0.05870.2846-0.00860.3225-21.8711-7.2885-61.7718
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 82 through 156 )
2X-RAY DIFFRACTION2chain 'A' and (resid 157 through 216 )
3X-RAY DIFFRACTION3chain 'A' and (resid 217 through 258 )
4X-RAY DIFFRACTION4chain 'A' and (resid 259 through 290 )
5X-RAY DIFFRACTION5chain 'A' and (resid 291 through 351 )
6X-RAY DIFFRACTION6chain 'A' and (resid 352 through 429 )
7X-RAY DIFFRACTION7chain 'A' and (resid 430 through 468 )

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