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- PDB-8dwb: Neuraminidase from influenza virus A/Moscow/10/1999(H3N2) in comp... -

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Basic information

Entry
Database: PDB / ID: 8dwb
TitleNeuraminidase from influenza virus A/Moscow/10/1999(H3N2) in complex with sialic acid
ComponentsNeuraminidase
KeywordsVIRAL PROTEIN / Hydrolase / neuraminidase / influenza
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
alpha-D-mannopyranose / N-acetyl-alpha-neuraminic acid / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.602 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: Cell Rep / Year: 2023
Title: Mutational fitness landscape of human influenza H3N2 neuraminidase.
Authors: Lei, R. / Hernandez Garcia, A. / Tan, T.J.C. / Teo, Q.W. / Wang, Y. / Zhang, X. / Luo, S. / Nair, S.K. / Peng, J. / Wu, N.C.
History
DepositionAug 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: 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 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 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

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Assembly

Deposited unit
AAA: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3108
Polymers43,2531
Non-polymers2,0577
Water4,342241
1
AAA: Neuraminidase
hetero molecules

AAA: Neuraminidase
hetero molecules

AAA: Neuraminidase
hetero molecules

AAA: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,24032
Polymers173,0134
Non-polymers8,22728
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 area26190 Å2
ΔGint-121 kcal/mol
Surface area47620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.217, 136.217, 150.155
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11AAA-1085-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Neuraminidase


Mass: 43253.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Moscow/10/1999(H3N2))
Strain: A/Moscow/10/1999(H3N2) / Gene: NA / Production host: unidentified baculovirus / References: UniProt: Q8AZ87, exo-alpha-sialidase

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Sugars , 4 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-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
#4: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 244 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 4.03 Å3/Da / Density % sol: 69.45 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 2.0 M NH4-sulfate, 0.2 M Li-sulfate, 0.1 M Tris pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12723 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12723 Å / Relative weight: 1
ReflectionResolution: 1.602→100.889 Å / Num. obs: 92200 / % possible obs: 100 % / Redundancy: 16 % / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Net I/σ(I): 14.6
Reflection shellResolution: 1.602→1.607 Å / Redundancy: 13.1 % / Rmerge(I) obs: 1.065 / Mean I/σ(I) obs: 2 / Num. unique obs: 923 / CC1/2: 0.913 / % possible all: 100

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Processing

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

2aep


Resolution: 1.602→100.889 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.027 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.059 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1819 4566 4.954 %
Rwork0.1693 87607 -
all0.17 --
obs-92173 99.957 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 17.492 Å2
Baniso -1Baniso -2Baniso -3
1--0.645 Å20 Å2-0 Å2
2---0.645 Å20 Å2
3---1.29 Å2
Refinement stepCycle: LAST / Resolution: 1.602→100.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2996 0 137 241 3374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0123282
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.684493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7715412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.33422.256164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40215517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3621520
X-RAY DIFFRACTIONr_chiral_restr0.1480.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022469
X-RAY DIFFRACTIONr_nbd_refined0.2270.21491
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22264
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2180
X-RAY DIFFRACTIONr_metal_ion_refined0.0860.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.160.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0790.221
X-RAY DIFFRACTIONr_mcbond_it1.2071.5581579
X-RAY DIFFRACTIONr_mcangle_it1.6472.3341980
X-RAY DIFFRACTIONr_scbond_it2.61.7931700
X-RAY DIFFRACTIONr_scangle_it3.6712.6122500
X-RAY DIFFRACTIONr_lrange_it3.77322.4615012
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.602-1.6430.2583160.22564150.22667360.9050.91199.92580.201
1.643-1.6880.1983560.19762210.19765780.9330.93499.98480.174
1.688-1.7370.2142990.17660780.17863780.9380.94599.98430.153
1.737-1.790.1983200.1659170.16262380.9490.95799.9840.139
1.79-1.8490.1692880.15157330.15160210.960.9641000.132
1.849-1.9140.1733160.14955320.1558480.9620.9671000.133
1.914-1.9860.1852830.15653510.15756340.9590.9651000.142
1.986-2.0670.1742580.16351790.16454380.9670.96799.98160.151
2.067-2.1590.1852720.16449470.16552190.9590.9641000.153
2.159-2.2650.192470.1747630.17250100.9580.9561000.161
2.265-2.3870.2061970.16545460.16647440.9530.96299.97890.157
2.387-2.5320.1712130.1743090.1745220.9620.9621000.165
2.532-2.7060.1842340.17640030.17642370.9570.961000.174
2.706-2.9230.2051810.19437940.19439760.9460.9599.97480.195
2.923-3.2020.1942020.18934550.1936590.9510.95599.94530.196
3.202-3.5790.1741680.17131650.17133340.9660.96599.970.187
3.579-4.1320.1471560.14827840.14829450.9730.97699.83020.171
4.132-5.0590.128990.13524320.13525310.9850.9821000.159
5.059-7.1450.1781010.17718870.17719880.9730.9711000.207
7.145-100.8890.226600.2210960.22111770.9680.96198.21580.273

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