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- PDB-9gqx: influenza neuraminidase mSN1 -

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Basic information

Entry
Database: PDB / ID: 9gqx
Titleinfluenza neuraminidase mSN1
ComponentsNeuraminidase
KeywordsVIRAL PROTEIN / influenza neuraminidase recombinant 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: 1.98 Å
AuthorsPramila, R. / Paesen, G.C. / Bowden, T.A.
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 10, 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)113,33412
Polymers111,2782
Non-polymers2,05610
Water11,151619
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,99224
Polymers222,5564
Non-polymers4,43620
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_545-y,x-1,z1
crystal symmetry operation4_655y+1,-x,z1
Buried area20450 Å2
ΔGint-142 kcal/mol
Surface area51400 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)226,34424
Polymers222,5564
Non-polymers3,78820
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 area20370 Å2
ΔGint-138 kcal/mol
Surface area49690 Å2
Unit cell
Length a, b, c (Å)92.165, 92.165, 147.903
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
Components on special symmetry positions
IDModelComponents
11A-1038-

HOH

21B-1015-

HOH

31B-1034-

HOH

41B-1043-

HOH

51B-1080-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 59 through 469 or resid 701 through 705))
d_2ens_1(chain "B" and (resid 59 through 469 or resid 701 through 705))

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_11ALAALALYSLYSAA59 - 469101 - 511
d_12CACACACAAE701
d_13CACACACAAF702
d_14NAGNAGNAGNAGAG703
d_15NAGNAGNAGNAGCC1
d_16NAGNAGNAGNAGCC2
d_21ALAALALYSLYSBB59 - 469101 - 511
d_22CACACACABI701
d_23CACACACABJ702
d_24NAGNAGNAGNAGBK703
d_25NAGNAGNAGNAGBL704
d_26NAGNAGNAGNAGDD1

NCS oper: (Code: givenMatrix: (0.234186526899, 0.972191345359, -0.000811558950392), (0.972189607276, -0.234187670493, -0.00187149495742), (-0.00200950830055, -0.000350710273076, -0.999997919437) ...NCS oper: (Code: given
Matrix: (0.234186526899, 0.972191345359, -0.000811558950392), (0.972189607276, -0.234187670493, -0.00187149495742), (-0.00200950830055, -0.000350710273076, -0.999997919437)
Vector: 34.1424070975, -55.6471403948, -162.074856666)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Neuraminidase


Mass: 55638.984 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

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Sugars , 3 types, 6 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#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.: 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
#5: 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: 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

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Non-polymers , 2 types, 623 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 619 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.82 Å3/Da / Density % sol: 56.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.03 M NaFl, 0.03 M NaBr, 0.03 M NaI, 0.1 M imidazole/MES pH6.5, 30% ethylene glycol/PEG 8K

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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: Dec 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 1.98→147.9 Å / Num. obs: 85857 / % possible obs: 100 % / Redundancy: 14.2 % / Biso Wilson estimate: 24.33 Å2 / CC1/2: 0.976 / Net I/σ(I): 2.8
Reflection shellResolution: 1.98→2.01 Å / Num. unique obs: 4278 / CC1/2: 0.342

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→92.17 Å / SU ML: 0.3303 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.0694
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2382 1935 2.31 %
Rwork0.2107 81937 -
obs0.2114 83872 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.52 Å2
Refinement stepCycle: LAST / Resolution: 1.98→92.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6296 0 127 619 7042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00296585
X-RAY DIFFRACTIONf_angle_d0.66988945
X-RAY DIFFRACTIONf_chiral_restr0.0498969
X-RAY DIFFRACTIONf_plane_restr0.00511152
X-RAY DIFFRACTIONf_dihedral_angle_d16.10472475
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 3.87420692926 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.030.468770.42034205X-RAY DIFFRACTION70.06
2.03-2.080.35861200.35015937X-RAY DIFFRACTION99.12
2.08-2.140.33871560.31975938X-RAY DIFFRACTION99.48
2.14-2.210.34031530.3065944X-RAY DIFFRACTION99.75
2.21-2.290.28731360.27385988X-RAY DIFFRACTION99.9
2.29-2.380.29691780.26925905X-RAY DIFFRACTION99.93
2.38-2.490.27881460.25475990X-RAY DIFFRACTION99.92
2.49-2.620.25951460.23675933X-RAY DIFFRACTION99.98
2.62-2.790.24381470.22796003X-RAY DIFFRACTION99.98
2.79-30.24381430.19665983X-RAY DIFFRACTION100
3-3.310.22551470.17735973X-RAY DIFFRACTION99.97
3.31-3.780.17451260.15136036X-RAY DIFFRACTION99.95
3.78-4.770.16451240.13676017X-RAY DIFFRACTION99.98
4.77-92.170.17831360.18086085X-RAY DIFFRACTION99.49

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