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- PDB-3lzf: Crystal Structure of Fab 2D1 in Complex with the 1918 Influenza V... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3lzf | |||||||||
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Title | Crystal Structure of Fab 2D1 in Complex with the 1918 Influenza Virus Hemagglutinin | |||||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / hemagglutinin / Fab / neutralizing antibodies / antibody / pandemic flu / swine flu / Envelope protein / Fusion protein / Glycoprotein / antigen / Virion / 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 / 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 / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ekiert, D.C. / Wilson, I.A. | |||||||||
![]() | ![]() Title: Structural basis of preexisting immunity to the 2009 H1N1 pandemic influenza virus. Authors: Xu, R. / Ekiert, D.C. / Krause, J.C. / Hai, R. / Crowe, J.E. / Wilson, I.A. | |||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 188.7 KB | Display | ![]() |
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PDB format | ![]() | 151.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
-Hemagglutinin, ... , 2 types, 2 molecules AB
#1: Protein | Mass: 36452.797 Da / Num. of mol.: 1 / Fragment: Ectodomain HA1, residues 18-344 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 20394.445 Da / Num. of mol.: 1 / Fragment: Ectodomain HA2, residues 345-520 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Antibody , 2 types, 2 molecules HL
#3: Antibody | Mass: 24699.842 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#4: Antibody | Mass: 22812.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Sugars , 3 types, 4 molecules ![](data/chem/img/NAG.gif)
#5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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 #7: Sugar | ChemComp-NAG / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.19 Å3/Da / Density % sol: 76.31 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: 16% PEG1000, 100mM PIPES pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0333 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 54245 / Num. obs: 53366 / % possible obs: 98.4 % / Observed criterion σ(I): 1 / Redundancy: 10.3 % / Biso Wilson estimate: 90.4 Å2 / Rsym value: 0.04 |
Reflection shell | Resolution: 2.8→2.89 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.49 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 82.287 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→49.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.872 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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