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- PDB-7u4g: Neuraminidase from influenza virus A/Shandong/9/1993(H3N2) -

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Basic information

Entry
Database: PDB / ID: 7u4g
TitleNeuraminidase from influenza virus A/Shandong/9/1993(H3N2)
ComponentsNeuraminidase
KeywordsVIRAL PROTEIN / Hydrolase / neuraminidase / influenza
Function / homology
Function and homology information


: / : / : / exo-alpha-sialidase / 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
ZANAMIVIR / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
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
A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4406
Polymers52,1871
Non-polymers2,2535
Water5,711317
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,76024
Polymers208,7474
Non-polymers9,01220
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area26120 Å2
ΔGint39 kcal/mol
Surface area49150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.954, 107.954, 78.619
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-871-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Neuraminidase


Mass: 52186.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Shandong/9/1993(H3N2))
Gene: NA / Production host: unidentified baculovirus / References: UniProt: Q98815, exo-alpha-sialidase

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Sugars , 4 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-f1_d2-e1WURCSPDB2Glycan 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]{}}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][a-D-Manp]{}}LINUCSPDB-CARE
#4: 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-ZMR / ZANAMIVIR / 4-GUANIDINO-2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / 4-guanidino-Neu5Ac2en / MODIFIED SIALIC ACID


Type: D-saccharide / Mass: 332.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20N4O7 / Comment: medication, antivirus, inhibitor*YM

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Non-polymers , 2 types, 318 molecules

#6: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.19 Å3/Da / Density % sol: 43.95 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 8% PEG-8000, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1272 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionResolution: 1.645→76.34 Å / Num. obs: 54981 / % possible obs: 96.8 % / Redundancy: 9.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.127 / Rrim(I) all: 0.138 / Net I/σ(I): 11.5
Reflection shellResolution: 1.645→1.65 Å / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.895 / Rrim(I) all: 0.834

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Processing

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

2aep


Resolution: 1.65→25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.338 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2147 2685 4.9 %RANDOM
Rwork0.1881 ---
obs0.1894 51828 96.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.35 Å2 / Biso mean: 19.373 Å2 / Biso min: 7.94 Å2
Baniso -1Baniso -2Baniso -3
1--2.14 Å20 Å20 Å2
2---2.14 Å20 Å2
3---4.29 Å2
Refinement stepCycle: final / Resolution: 1.65→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3016 0 149 317 3482
Biso mean--33.06 26.27 -
Num. residues----388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0123255
X-RAY DIFFRACTIONr_angle_refined_deg1.211.6974437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8015387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.31421.429168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51615503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7041523
X-RAY DIFFRACTIONr_chiral_restr0.0910.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022437
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 209 -
Rwork0.314 3821 -
all-4030 -
obs--98.03 %

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