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- PDB-9gqq: influenza neuraminidase N1/19 hybrid -

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Basic information

Entry
Database: PDB / ID: 9gqq
Titleinfluenza neuraminidase N1/19 hybrid
ComponentsNeuraminidase
KeywordsVIRAL PROTEIN / influenza virus neuraminidase loop grafting
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 speciesunidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsBowden, T.A. / Paesen, G.C. / Rijal, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/S007555/1 United Kingdom
Citation
Journal: Elife / Year: 2025
Title: Structure-guided loop grafting improves expression and stability of influenza neuraminidase for vaccine development.
Authors: Rijal, P. / Wei, L. / Paesen, G.C. / Stuart, D.I. / Haworth, M. / Huang, K.A. / Bowden, T.A. / Townsend, A.R.M.
#1: Journal: Elife / Year: 2025
Title: Structure-Guided Loop Grafting Improves Expression and Stability of Influenza Neuraminidase for Vaccine Development
Authors: Rijal, P. / Wei, L. / Paesen, G.C. / Stuart, D.I. / Howarth, M.R. / Huang, K.Y.A. / Bowden, T.A. / Townsend, A.R.
History
DepositionSep 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase
B: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,29213
Polymers111,3812
Non-polymers1,91211
Water8,539474
1
A: Neuraminidase
B: Neuraminidase
hetero molecules

A: Neuraminidase
B: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,58526
Polymers222,7614
Non-polymers3,82422
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area19100 Å2
ΔGint-133 kcal/mol
Surface area49080 Å2
Unit cell
Length a, b, c (Å)115.412, 234.367, 115.651
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 65 through 469 or resid 700 through 708))
d_2ens_1chain "B"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ILEILELYSLYSAA65 - 469107 - 511
d_12CACACACAAD501
d_13CACACACAAE502
d_14NAGNAGNAGNAGAF503
d_15NAGNAGNAGNAGCC1
d_16NAGNAGNAGNAGCC2
d_21ILEILELYSLYSBB65 - 469107 - 511
d_22CACACACABI501
d_23CACACACABJ502
d_24NAGNAGNAGNAGBK503
d_25NAGNAGNAGNAGBL504
d_26NAGNAGNAGNAGBM505

NCS oper: (Code: givenMatrix: (0.00378203568205, -0.00568210796281, 0.999976704656), (-0.0023123053414, 0.999981133395, 0.005690878553), (-0.999990174677, -0.0023337745812, 0.00376882555929)Vector: ...NCS oper: (Code: given
Matrix: (0.00378203568205, -0.00568210796281, 0.999976704656), (-0.0023123053414, 0.999981133395, 0.005690878553), (-0.999990174677, -0.0023337745812, 0.00376882555929)
Vector: 86.6697472638, -0.137362630438, 28.8394326957)

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Components

#1: Protein Neuraminidase


Mass: 55690.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified influenza virus / Gene: NA / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: A0A024CWJ7, exo-alpha-sialidase
#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: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#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: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 3.51 Å3/Da / Density % sol: 64.96 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 5% PGA_LM, 30% PEG550 MME, 0.1M Tris pH 7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 6199 Å
DetectorType: DECTRIS EIGER2 X CdTe 9M / Detector: PIXEL / Date: Sep 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 6199 Å / Relative weight: 1
ReflectionResolution: 1.775→82.314 Å / Num. obs: 58546 / % possible obs: 94.2 % / Redundancy: 13.4 % / Biso Wilson estimate: 24.66 Å2 / CC1/2: 0.9888 / Net I/σ(I): 5.4
Reflection shellResolution: 1.775→1.981 Å / Num. unique obs: 2927 / CC1/2: 0.564

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→64.69 Å / SU ML: 0.1997 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9701
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2146 1999 3.42 %RANDOM
Rwork0.1888 56508 --
obs0.1897 58507 38.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.42 Å2
Refinement stepCycle: LAST / Resolution: 1.78→64.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6164 0 116 474 6754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00356438
X-RAY DIFFRACTIONf_angle_d0.7058734
X-RAY DIFFRACTIONf_chiral_restr0.0516940
X-RAY DIFFRACTIONf_plane_restr0.00461122
X-RAY DIFFRACTIONf_dihedral_angle_d14.05342420
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 4.01844448341 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.820.364930.257472X-RAY DIFFRACTION0.72
1.82-1.870.289120.2676357X-RAY DIFFRACTION3.49
1.87-1.920.3373310.2731869X-RAY DIFFRACTION8.44
1.92-1.990.3334600.23991702X-RAY DIFFRACTION16.53
1.99-2.060.3094840.24552379X-RAY DIFFRACTION23.09
2.06-2.140.27671040.22732926X-RAY DIFFRACTION28.29
2.14-2.240.2631160.24533290X-RAY DIFFRACTION31.87
2.24-2.350.24691300.25123648X-RAY DIFFRACTION35.3
2.35-2.50.28681420.24214055X-RAY DIFFRACTION39.12
2.5-2.70.26751660.23774682X-RAY DIFFRACTION45.15
2.7-2.970.22642000.20925660X-RAY DIFFRACTION54.29
2.97-3.40.21462530.17977114X-RAY DIFFRACTION68.18
3.4-4.280.1793190.15219033X-RAY DIFFRACTION85.96
4.28-64.690.18273790.167710721X-RAY DIFFRACTION99.3

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