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- PDB-5wko: Crystal structure of antibody 27F3 recognizing the HA from A/Cali... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5wko | ||||||
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Title | Crystal structure of antibody 27F3 recognizing the HA from A/California/04/2009 (H1N1) influenza virus | ||||||
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![]() | ANTIVIRAL PROTEIN / 27F3 H1 HA A/California/04/2009 | ||||||
Function / homology | ![]() immunoglobulin complex, circulating / immunoglobulin receptor binding / viral budding from plasma membrane / complement activation, classical pathway / antigen binding / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / blood microparticle / host cell surface receptor binding ...immunoglobulin complex, circulating / immunoglobulin receptor binding / viral budding from plasma membrane / complement activation, classical pathway / antigen binding / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / blood microparticle / host cell surface receptor binding / immune response / 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 / extracellular space / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wilson, I.A. / Lang, S. / Zhu, X. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Antibody 27F3 Broadly Targets Influenza A Group 1 and 2 Hemagglutinins through a Further Variation in VH1-69 Antibody Orientation on the HA Stem. Authors: Lang, S. / Xie, J. / Zhu, X. / Wu, N.C. / Lerner, R.A. / 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 | ![]() | 2 MB | Display | ![]() |
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PDB format | ![]() | 1.7 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 643.5 KB | Display | ![]() |
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Full document | ![]() | 808.9 KB | Display | |
Data in XML | ![]() | 192.1 KB | Display | |
Data in CIF | ![]() | 259.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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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Unit cell |
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Components
#1: Antibody | Mass: 23817.703 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 23140.697 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Protein | Mass: 36729.402 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 20206.320 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.72 Å3/Da / Density % sol: 78.51 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 1.6 M ammonium sulfate, 0.1 M citric acid pH 4.0 |
-Data collection
Diffraction | Mean temperature: 77.2 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 177944 / % possible obs: 97 % / Redundancy: 5.7 % / CC1/2: 0.97 / Rpim(I) all: 0.08 / Rsym value: 0.13 / Net I/av σ(I): 8.7 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 3.5→3.56 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 8765 / CC1/2: 0.73 / Rpim(I) all: 0.45 / Rsym value: 0.76 / % possible all: 94.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4M4Y 4FQH 4FQL Resolution: 3.492→49.451 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.45 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.492→49.451 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 98.7608 Å / Origin y: 0.2239 Å / Origin z: 46.8985 Å
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Refinement TLS group | Selection details: all |