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- PDB-9gqt: influenza neuraminidase hybrid N1/09 -

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Basic information

Entry
Database: PDB / ID: 9gqt
Titleinfluenza neuraminidase hybrid N1/09
ComponentsNeuraminidase
KeywordsVIRAL PROTEIN / influenza neuraminidase hybrid expression
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: 1.94 Å
AuthorsBowden, T.A. / Paesen, G.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/S007555/1 United Kingdom
CitationJournal: 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

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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)112,97112
Polymers111,2802
Non-polymers1,69110
Water12,520695
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,34824
Polymers222,5604
Non-polymers3,78820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area21360 Å2
ΔGint-145 kcal/mol
Surface area50310 Å2
2
B: Neuraminidase
hetero molecules

B: Neuraminidase
hetero molecules

B: Neuraminidase
hetero molecules

B: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,53524
Polymers222,5604
Non-polymers2,97520
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 area18150 Å2
ΔGint-149 kcal/mol
Surface area47320 Å2
Unit cell
Length a, b, c (Å)92.089, 92.089, 146.804
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4
Space group name HallP4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 66 through 167 or resid 169 through 469 or resid 500 through 504))
d_2ens_1(chain "B" and (resid 66 through 167 or resid 169 through 469 or resid 500 through 504))

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_11ILEILEPROPROAA66 - 167108 - 209
d_12PROPROLYSLYSAA169 - 469211 - 511
d_13CACACACAAD500
d_14CACACACAAE501
d_15NAGNAGNAGNAGAF502
d_16NAGNAGNAGNAGAG503
d_17NAGNAGNAGNAGCC1
d_21ILEILEPROPROBB66 - 167108 - 209
d_22PROPROLYSLYSBB169 - 469211 - 511
d_23CACACACABH500
d_24CACACACABI501
d_25NAGNAGNAGNAGBJ502
d_26NAGNAGNAGNAGBK503
d_27NAGNAGNAGNAGBL504

NCS oper: (Code: givenMatrix: (-0.24237459611, -0.970160420626, 0.00658129249009), (-0.970178660614, 0.242387678914, 0.00125682142208), (-0.00281454261042, -0.00608040794858, -0.999977553243)Vector: ...NCS oper: (Code: given
Matrix: (-0.24237459611, -0.970160420626, 0.00658129249009), (-0.970178660614, 0.242387678914, 0.00125682142208), (-0.00281454261042, -0.00608040794858, -0.999977553243)
Vector: 56.0578399674, 33.5607218547, -104.731255751)

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Components

#1: Protein Neuraminidase


Mass: 55640.086 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: obtained synthetically / 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.: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / 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: 2.8 Å3/Da / Density % sol: 56.02 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 25% w/v pentaerythritol ethoxylate 797, 100 mM MES pH 6.5, 50 mM magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6199 Å
DetectorType: DECTRIS EIGER2 X CdTe 9M / Detector: PIXEL / Date: Oct 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 1.94→41.18 Å / Num. obs: 90312 / % possible obs: 99.9 % / Redundancy: 13.9 % / Biso Wilson estimate: 19.98 Å2 / CC1/2: 0.983 / Net I/σ(I): 4.1
Reflection shellResolution: 1.94→1.97 Å / Num. unique obs: 4440 / CC1/2: 0.282

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→39.12 Å / SU ML: 0.2694 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.277
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2122 1948 2.17 %
Rwork0.1826 88022 -
obs0.1832 89970 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.73 Å2
Refinement stepCycle: LAST / Resolution: 1.94→39.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6273 0 102 695 7070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01286543
X-RAY DIFFRACTIONf_angle_d1.15418887
X-RAY DIFFRACTIONf_chiral_restr0.0678955
X-RAY DIFFRACTIONf_plane_restr0.00951150
X-RAY DIFFRACTIONf_dihedral_angle_d15.6362439
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.466204415741 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.990.34131140.34026171X-RAY DIFFRACTION97.87
1.99-2.040.39151480.36436116X-RAY DIFFRACTION96.7
2.04-2.10.29661250.26646310X-RAY DIFFRACTION99.84
2.1-2.170.30171620.24476231X-RAY DIFFRACTION99.83
2.17-2.250.27011440.22286320X-RAY DIFFRACTION99.97
2.25-2.340.2811290.20696293X-RAY DIFFRACTION99.94
2.34-2.440.25761470.2016271X-RAY DIFFRACTION99.92
2.44-2.570.23041450.19236304X-RAY DIFFRACTION99.97
2.57-2.730.24091340.18486309X-RAY DIFFRACTION99.98
2.73-2.940.20421020.15376356X-RAY DIFFRACTION99.97
2.94-3.240.17241490.15436287X-RAY DIFFRACTION100
3.24-3.710.15011410.13326344X-RAY DIFFRACTION99.95
3.71-4.670.14841550.12146332X-RAY DIFFRACTION100
4.67-39.120.17051530.16096378X-RAY DIFFRACTION99.68

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