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

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Basic information

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


exo-alpha-sialidase / exo-alpha-sialidase activity / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Chem-G39 / Neuraminidase
Similarity search - Component
Biological speciesWuhan spiny eel influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 24, 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 1.3Nov 6, 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)88,7938
Polymers87,7022
Non-polymers1,0916
Water13,529751
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,58716
Polymers175,4044
Non-polymers2,18312
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 area17840 Å2
ΔGint-58 kcal/mol
Surface area43420 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)177,58716
Polymers175,4044
Non-polymers2,18312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
Buried area17840 Å2
ΔGint-62 kcal/mol
Surface area43990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.417, 126.417, 110.478
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-604-

HOH

21A-619-

HOH

31A-908-

HOH

41A-915-

HOH

51A-919-

HOH

61B-615-

HOH

71B-910-

HOH

81B-925-

HOH

91B-931-

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_14G39G39G39G39AC501
d_15NAGNAGNAGNAGAD502
d_21GLUGLUTRPTRPBB84 - 8516 - 17
d_22PHEPHETHRTHRBB87 - 9119 - 23
d_23PROPROVALVALBB93 - 47225 - 404
d_24G39G39G39G39BF501
d_25NAGNAGNAGNAGBG502

NCS oper: (Code: givenMatrix: (-0.507275279985, 0.861783837498, 0.000638548147142), (0.861783682445, 0.50727420382, 0.00132921390038), (0.000821576052979, 0.00122456772714, -0.999998912723)Vector: - ...NCS oper: (Code: given
Matrix: (-0.507275279985, 0.861783837498, 0.000638548147142), (0.861783682445, 0.50727420382, 0.00132921390038), (0.000821576052979, 0.00122456772714, -0.999998912723)
Vector: -63.1483982983, 63.1289049414, -23.2801572762)

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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-G39 / (3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid / Oseltamivir carboxylate


Mass: 284.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H24N2O4 / Comment: medication, antivirus*YM
#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.: 751 / 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: 2.52 Å3/Da / Density % sol: 51.12 %
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 oseltamivir 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: 1.6→50 Å / Num. obs: 96777 / % possible obs: 85.3 % / Redundancy: 7.4 % / Biso Wilson estimate: 14.38 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.056 / Net I/σ(I): 11
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 2.4 / CC1/2: 0.818 / Rpim(I) all: 0.488 / % possible all: 100

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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: 1.6→41.59 Å / SU ML: 0.1443 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.6354
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1804 4718 4.88 %
Rwork0.1576 92011 -
obs0.1587 96729 85.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.18 Å2
Refinement stepCycle: LAST / Resolution: 1.6→41.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5910 0 70 751 6731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00626124
X-RAY DIFFRACTIONf_angle_d0.91398329
X-RAY DIFFRACTIONf_chiral_restr0.0617943
X-RAY DIFFRACTIONf_plane_restr0.00881079
X-RAY DIFFRACTIONf_dihedral_angle_d12.00862223
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.392474789391 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.24511620.22233619X-RAY DIFFRACTION99.92
1.62-1.640.22692080.22023562X-RAY DIFFRACTION99.95
1.64-1.660.26121940.21753577X-RAY DIFFRACTION99.97
1.66-1.680.2291890.21693537X-RAY DIFFRACTION99.92
1.68-1.70.23271900.20873584X-RAY DIFFRACTION100
1.7-1.730.3056560.21551424X-RAY DIFFRACTION39.18
1.73-1.750.22951810.18663573X-RAY DIFFRACTION99.95
1.75-1.780.21511740.18033618X-RAY DIFFRACTION99.87
1.78-1.810.20481920.18163590X-RAY DIFFRACTION99.97
1.81-1.840.23221660.17433585X-RAY DIFFRACTION99.71
1.84-1.870.22421780.17053578X-RAY DIFFRACTION99.81
1.87-1.90.2058480.1931721X-RAY DIFFRACTION20.42
1.9-1.940.21391330.17282114X-RAY DIFFRACTION59.4
1.94-1.980.20991300.16052132X-RAY DIFFRACTION60.35
1.98-2.020.17772180.15153551X-RAY DIFFRACTION99.47
2.02-2.040.1745570.15991317X-RAY DIFFRACTION93.53
2.09-2.120.1688940.14662022X-RAY DIFFRACTION99.62
2.12-2.180.18021590.15093625X-RAY DIFFRACTION99.89
2.18-2.240.17251780.15353511X-RAY DIFFRACTION98.77
2.27-2.310.1516960.15052160X-RAY DIFFRACTION99.34
2.31-2.390.16351590.1513647X-RAY DIFFRACTION99.95
2.39-2.490.18932030.15833568X-RAY DIFFRACTION99.95
2.49-2.60.18511680.16423603X-RAY DIFFRACTION99.84
2.6-2.740.18861690.16592704X-RAY DIFFRACTION76.09
2.74-2.910.1931980.15963625X-RAY DIFFRACTION99.77
2.91-3.140.17781610.15253585X-RAY DIFFRACTION99.57
3.14-3.410.17651750.13733148X-RAY DIFFRACTION98.61
3.48-3.950.14621200.13162416X-RAY DIFFRACTION71.96
3.95-4.980.12571850.11933639X-RAY DIFFRACTION99.82
4.98-41.590.16861770.17063676X-RAY DIFFRACTION99.64
Refinement TLS params.Method: refined / Origin x: -22.8391579352 Å / Origin y: 46.822349289 Å / Origin z: -11.6147800353 Å
111213212223313233
T0.104401033993 Å2-0.00310473794347 Å20.0117409269875 Å2-0.104195426076 Å20.00136824634476 Å2--0.128445842642 Å2
L0.139897856456 °2-0.249026790342 °2-0.0430968265025 °2-0.233661009659 °20.0901187709547 °2---0.007478873314 °2
S0.0037885375679 Å °0.000110711669199 Å °0.0431722459703 Å °-0.0105255816192 Å °0.00794063407145 Å °-0.0503505795228 Å °-0.00370745741362 Å °0.00494302353748 Å °-0.00923940895573 Å °
Refinement TLS groupSelection details: all

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