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- PDB-7u4e: Neuraminidase from influenza virus A/Bilthoven/17938/1969(H3N2) -

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Basic information

Entry
Database: PDB / ID: 7u4e
TitleNeuraminidase from influenza virus A/Bilthoven/17938/1969(H3N2)
ComponentsNeuraminidase
KeywordsVIRAL PROTEIN / Hydrolase / neuraminidase / influenza
Function / homology
Function and homology information


exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / membrane => GO:0016020 / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsLei, R. / Hernandez Garcia, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R00 AI139445 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)DP2 AT011966 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI167910 United States
CitationJournal: Nat Commun / Year: 2022
Title: Prevalence and mechanisms of evolutionary contingency in human influenza H3N2 neuraminidase.
Authors: Lei, R. / Tan, T.J.C. / Hernandez Garcia, A. / Wang, Y. / Diefenbacher, M. / Teo, C. / Gopan, G. / Tavakoli Dargani, Z. / Teo, Q.W. / Graham, C.S. / Brooke, C.B. / Nair, S.K. / Wu, N.C.
History
DepositionFeb 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase
B: Neuraminidase
C: Neuraminidase
D: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,50120
Polymers209,2114
Non-polymers6,29016
Water36,1022004
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23160 Å2
ΔGint23 kcal/mol
Surface area46930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.339, 137.944, 138.246
Angle α, β, γ (deg.)90.000, 92.150, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-733-

HOH

21C-1041-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Neuraminidase /


Mass: 52302.812 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Bilthoven/17938/1969(H3N2))
Strain: A/Bilthoven/17938/1969(H3N2) / Gene: NA / Production host: unidentified baculovirus / References: UniProt: H9XI12, exo-alpha-sialidase

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Sugars , 2 types, 8 molecules

#2: Polysaccharide
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_d2-e1_e2-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / 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

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Non-polymers , 3 types, 2012 molecules

#3: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 2004 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.65 Å3/Da / Density % sol: 53.57 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 10% PEG-6000, 5% MPD, 0.1 M HEPES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 20, 2021
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.54→46.049 Å / Num. obs: 322550 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.111 / Net I/σ(I): 12.1
Reflection shellResolution: 1.54→1.563 Å / Rmerge(I) obs: 0.989 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 322494 / CC1/2: 0.778 / Rrim(I) all: 1.064

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AEP

2aep


Resolution: 1.54→25 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.223 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1803 16240 5.1 %RANDOM
Rwork0.1658 ---
obs0.1665 304302 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 79.84 Å2 / Biso mean: 17.195 Å2 / Biso min: 9.51 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å20.09 Å2
2---0.52 Å2-0 Å2
3----0.98 Å2
Refinement stepCycle: final / Resolution: 1.54→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12108 0 408 2004 14520
Biso mean--25.47 29.75 -
Num. residues----1552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01212918
X-RAY DIFFRACTIONr_angle_refined_deg0.9951.67417567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.69751567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.06521.51702
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.994152019
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.38715104
X-RAY DIFFRACTIONr_chiral_restr0.0770.21739
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029800
LS refinement shellResolution: 1.54→1.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 1156 -
Rwork0.246 22450 -
all-23606 -
obs--100 %

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