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- PDB-5gjt: Crystal structure of H1 hemagglutinin from A/Washington/05/2011 i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5gjt | |||||||||
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Title | Crystal structure of H1 hemagglutinin from A/Washington/05/2011 in complex with a neutralizing antibody 3E1 | |||||||||
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![]() | IMMUNE SYSTEM / epitope / Fab / complementarity determining region / paratope | |||||||||
Function / homology | ![]() viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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 | ![]() ![]() ![]() | |||||||||
![]() | Wang, W. / Zhang, T. / Ding, J. | |||||||||
![]() | ![]() Title: Human antibody 3E1 targets the HA stem region of H1N1 and H5N6 influenza A viruses Authors: Wang, W. / Sun, X. / Li, Y. / Su, J. / Ling, Z. / Zhang, T. / Wang, F. / Zhang, H. / Chen, H. / Ding, J. / Sun, B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 190.7 KB | Display | ![]() |
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PDB format | ![]() | 148.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 768.5 KB | Display | ![]() |
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Full document | ![]() | 775 KB | Display | |
Data in XML | ![]() | 31.3 KB | Display | |
Data in CIF | ![]() | 43.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5gjsSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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
#1: Protein | Mass: 36507.160 Da / Num. of mol.: 1 / Fragment: UNP residues 1344 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 20869.203 Da / Num. of mol.: 1 / Fragment: hemagglutinin Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Antibody | Mass: 23483.084 Da / Num. of mol.: 1 / Fragment: light chain of neutralizing antibody 3E1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Antibody | Mass: 23663.646 Da / Num. of mol.: 1 / Fragment: heavy chain of neutralizing antibody 3E1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#5: 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 |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.44 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Na HEPES, 20% PEG400 and 0.1M LiCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: CMOS / Date: Jan 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 22417 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 62.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.9 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5GJS Resolution: 3.1→50 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.859 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.474 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.49 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→50 Å
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Refine LS restraints |
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