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- PDB-8gv7: Crystal structure of PN-SIA28 in complex with influenza hemagglut... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8gv7 | ||||||
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Title | Crystal structure of PN-SIA28 in complex with influenza hemagglutinin H18 A/flat-faced bat/Peru/033/2010 | ||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / Influenza / hemagglutinin / antibody / broadly neutralizing / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, Y. / Song, H. / Qi, J. / Gao, G.F. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural basis for a human broadly neutralizing influenza A hemagglutinin stem-specific antibody including H17/18 subtypes. Authors: Chen, Y. / Wang, F. / Yin, L. / Jiang, H. / Lu, X. / Bi, Y. / Zhang, W. / Shi, Y. / Burioni, R. / Tong, Z. / Song, H. / Qi, J. / Gao, G.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203 KB | Display | ![]() |
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PDB format | ![]() | 128 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 632.1 KB | Display | ![]() |
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Full document | ![]() | 635.3 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 24.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wvdC ![]() 7wvgC ![]() 7wviC ![]() 8gv4C ![]() 8gv5C ![]() 8gv6C ![]() 5gjsS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Hemagglutinin H18- ... , 2 types, 2 molecules AB
#1: Protein | Mass: 36406.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: HA / Production host: ![]() |
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#2: Protein | Mass: 20122.459 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: HA / Production host: ![]() |
-Antibody , 2 types, 2 molecules CD
#3: Antibody | Mass: 13588.259 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#4: Antibody | Mass: 11527.934 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Sugars , 4 types, 5 molecules ![](data/chem/img/NAG.gif)
#5: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#7: 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 Source method: isolated from a genetically manipulated source |
#8: Sugar |
-Non-polymers , 1 types, 223 molecules ![](data/chem/img/HOH.gif)
#9: Water | ChemComp-HOH / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.82 Å3/Da / Density % sol: 81.97 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis Tris 25 % w/v PEG 3350(pH 5.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 3, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 66862 / % possible obs: 94.1 % / Redundancy: 16.5 % / Biso Wilson estimate: 41.66 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 19.83 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 1.68 / Mean I/σ(I) obs: 1.66 / Num. unique obs: 6653 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5GJS Resolution: 2.6→45.97 Å / SU ML: 0.2955 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.7349 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→45.97 Å
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Refine LS restraints |
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LS refinement shell |
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