+Open data
-Basic information
Entry | Database: PDB / ID: 7u4e | ||||||||||||
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Title | Neuraminidase from influenza virus A/Bilthoven/17938/1969(H3N2) | ||||||||||||
Components | Neuraminidase | ||||||||||||
Keywords | VIRAL 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 | ||||||||||||
Biological species | Influenza A virus | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å | ||||||||||||
Authors | Lei, R. / Hernandez Garcia, A. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u4e.cif.gz | 366.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u4e.ent.gz | 292.1 KB | Display | PDB format |
PDBx/mmJSON format | 7u4e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7u4e_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7u4e_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7u4e_validation.xml.gz | 76.9 KB | Display | |
Data in CIF | 7u4e_validation.cif.gz | 115.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/7u4e ftp://data.pdbj.org/pub/pdb/validation_reports/u4/7u4e | HTTPS FTP |
-Related structure data
Related structure data | 7u4fC 7u4gC 2aepS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | 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 Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 2012 molecules
#3: Chemical | ChemComp-EPE / #5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.57 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 10% PEG-6000, 5% MPD, 0.1 M HEPES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 20, 2021 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.84 Å2 / Biso mean: 17.195 Å2 / Biso min: 9.51 Å2
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Refinement step | Cycle: final / Resolution: 1.54→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.54→1.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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