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- PDB-7xvw: Structure of neuraminidase from influenza B-like viruses derived ... -

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Basic information

Entry
Database: PDB / ID: 7xvw
TitleStructure of neuraminidase from influenza B-like viruses derived from spiny eel
ComponentsNeuraminidase
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Chem-BCZ / Neuraminidase
Similarity search - Component
Biological speciesWuhan spiny eel influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsChai, Y. / Gao, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31872745 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structural and inhibitor sensitivity analysis of influenza B-like viral neuraminidases derived from Asiatic toad and spiny eel.
Authors: Li, L. / Chai, Y. / Peng, W. / Li, D. / Sun, L. / Gao, G.F. / Qi, J. / Xiao, H. / Liu, W.J. / von Itzstein, M. / Gao, F.
History
DepositionMay 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)88,8828
Polymers87,7022
Non-polymers1,1796
Water12,106672
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,76316
Polymers175,4044
Non-polymers2,35912
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 area18060 Å2
ΔGint-43 kcal/mol
Surface area42700 Å2
MethodPISA
2
B: Neuraminidase
hetero molecules

B: Neuraminidase
hetero molecules

B: Neuraminidase
hetero molecules

B: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,76316
Polymers175,4044
Non-polymers2,35912
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 area18020 Å2
ΔGint-39 kcal/mol
Surface area43140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.085, 126.085, 110.432
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-630-

HOH

21A-876-

HOH

31A-888-

HOH

41B-607-

HOH

51B-872-

HOH

61B-877-

HOH

71B-896-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 84 through 85 or resid 87...
d_2ens_1(chain "B" and (resid 84 through 85 or resid 87...

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_11GLUGLUTRPTRPAA84 - 8516 - 17
d_12PHEPHETHRTHRAA87 - 9119 - 23
d_13PROPROVALVALAA93 - 47225 - 404
d_14BCZBCZBCZBCZAC501
d_15NAGNAGNAGNAGAD502
d_21GLUGLUTRPTRPBB84 - 8516 - 17
d_22PHEPHETHRTHRBB87 - 9119 - 23
d_23PROPROVALVALBB93 - 47225 - 404
d_24BCZBCZNAGNAGBF - G501 - 502
d_25BCZBCZNAGNAGBF - G501 - 502

NCS oper: (Code: givenMatrix: (-0.507428886547, -0.861692483304, 0.00141043103651), (-0.861693401184, 0.507426855071, -0.00157133940061), (0.000638320765071, -0.00201270211942, -0.999997770786)Vector: ...NCS oper: (Code: given
Matrix: (-0.507428886547, -0.861692483304, 0.00141043103651), (-0.861693401184, 0.507426855071, -0.00157133940061), (0.000638320765071, -0.00201270211942, -0.999997770786)
Vector: 63.046230266, 62.9038289687, -87.7083239966)

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Components

#1: Protein Neuraminidase


Mass: 43851.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wuhan spiny eel influenza virus / Gene: NA / Plasmid: pFastBac1 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: A0A2P1GNP4, exo-alpha-sialidase
#2: Chemical ChemComp-BCZ / 3-(1-ACETYLAMINO-2-ETHYL-BUTYL)-4-GUANIDINO-2-HYDROXY-CYCLOPENTANECARBOXYLIC ACID / BCX-1812


Mass: 328.407 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H28N4O4
#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.: 2 / 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
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / Source method: isolated from a natural source / Formula: H2O
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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 4.0 M Potassium formate, 0.1 M BIS-TRIS propane pH 9.0, 2% w/v Polyethylene glycol monomethyl ether 2,000. NA crystals were soaked in 10 mM zanamivir, oseltamivir and peramivir for 30 min.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 60070 / % possible obs: 93.7 % / Redundancy: 13.9 % / Biso Wilson estimate: 16.59 Å2 / CC1/2: 0.9931 / Rpim(I) all: 0.102 / Net I/σ(I): 8.3
Reflection shellResolution: 1.94→2.04 Å / CC1/2: 0.815 / Rpim(I) all: 0.446

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XVR

7xvr


Resolution: 1.94→39.87 Å / SU ML: 0.1829 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.1726
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1903 2958 4.95 %
Rwork0.1566 56743 -
obs0.1583 59701 93.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.37 Å2
Refinement stepCycle: LAST / Resolution: 1.94→39.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5910 0 76 672 6658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00756130
X-RAY DIFFRACTIONf_angle_d0.9248339
X-RAY DIFFRACTIONf_chiral_restr0.0598947
X-RAY DIFFRACTIONf_plane_restr0.0091081
X-RAY DIFFRACTIONf_dihedral_angle_d11.79822215
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.371707313697 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.970.24861660.20462852X-RAY DIFFRACTION100
1.97-2.010.22291470.19622863X-RAY DIFFRACTION100
2.01-2.040.23371610.18542870X-RAY DIFFRACTION99.97
2.04-2.080.22881000.19331504X-RAY DIFFRACTION53.47
2.08-2.120.21351420.16612880X-RAY DIFFRACTION99.97
2.12-2.170.18451700.16592873X-RAY DIFFRACTION100
2.17-2.220.20451550.16372849X-RAY DIFFRACTION100
2.22-2.280.216550.16541303X-RAY DIFFRACTION44.32
2.28-2.340.22191290.1612882X-RAY DIFFRACTION100
2.34-2.410.19261290.16272895X-RAY DIFFRACTION99.97
2.41-2.480.22081570.1672859X-RAY DIFFRACTION100
2.48-2.570.18731870.16932874X-RAY DIFFRACTION100
2.57-2.680.22881370.1652889X-RAY DIFFRACTION99.87
2.68-2.80.21511530.16272871X-RAY DIFFRACTION100
2.8-2.950.19971500.16142890X-RAY DIFFRACTION100
2.95-3.130.20071430.15442897X-RAY DIFFRACTION99.97
3.13-3.370.17981340.1432920X-RAY DIFFRACTION100
3.37-3.710.16521190.142415X-RAY DIFFRACTION83.14
3.71-4.250.13381270.12562490X-RAY DIFFRACTION86.09
4.25-5.340.14671520.11992904X-RAY DIFFRACTION99.97
5.35-39.870.19541450.18022963X-RAY DIFFRACTION99.58
Refinement TLS params.Method: refined / Origin x: 22.8264588443 Å / Origin y: 46.6675220435 Å / Origin z: -43.8644947928 Å
111213212223313233
T0.146596360933 Å20.00474465238878 Å20.0115862193355 Å2-0.154060207715 Å2-0.00289901354862 Å2--0.160197456791 Å2
L0.183920978352 °20.304209604654 °2-0.0512352895191 °2-0.352405732116 °2-0.111077523761 °2--0.0143092738298 °2
S0.00383800345663 Å °0.0030982917119 Å °0.0483934198382 Å °0.00870209339899 Å °0.00436475837695 Å °0.0605630900775 Å °-0.00840746910448 Å °-0.00499022330325 Å °-0.00784178770523 Å °
Refinement TLS groupSelection details: all

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