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- PDB-4r8w: Crystal structure of H7 hemagglutinin from A/Anhui/1/2013 in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4r8w | ||||||
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Title | Crystal structure of H7 hemagglutinin from A/Anhui/1/2013 in complex with a neutralizing antibody CT149 | ||||||
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Function / homology | ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wu, Y. / Shi, Y. / Qi, J. / Gao, G.F. | ||||||
![]() | ![]() Title: A potent broad-spectrum protective human monoclonal antibody crosslinking two haemagglutinin monomers of influenza A virus Authors: Wu, Y. / Cho, M. / Shore, D. / Song, M. / Choi, J. / Jiang, T. / Deng, Y.Q. / Bourgeois, M. / Almli, L. / Yang, H. / Chen, L.M. / Shi, Y. / Qi, J. / Li, A. / Yi, K.S. / Chang, M. / Bae, J.S. ...Authors: Wu, Y. / Cho, M. / Shore, D. / Song, M. / Choi, J. / Jiang, T. / Deng, Y.Q. / Bourgeois, M. / Almli, L. / Yang, H. / Chen, L.M. / Shi, Y. / Qi, J. / Li, A. / Yi, K.S. / Chang, M. / Bae, J.S. / Lee, H. / Shin, J. / Stevens, J. / Hong, S. / Qin, C.F. / Gao, G.F. / Chang, S.J. / Donis, R.O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 299.4 KB | Display | ![]() |
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PDB format | ![]() | 241.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4ubdC ![]() 4dn3S ![]() 4kolS 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 on special symmetry positions |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | ![]() Mass: 34993.559 Da / Num. of mol.: 1 / Fragment: UNP residues 19-339 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: HA / Production host: ![]() ![]() ![]() |
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#2: Protein | ![]() Mass: 20442.463 Da / Num. of mol.: 1 / Fragment: UNP residues 340-516 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: HA / Production host: ![]() ![]() ![]() |
-Antibody , 2 types, 2 molecules HL
#3: Antibody | Mass: 24429.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#4: Antibody | Mass: 23761.348 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
-Sugars / Non-polymers , 2 types, 28 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Sugar | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.81 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion / pH: 8.5 Details: 30% v/v PEG 4000, 60mM Divalents, pH 8.5, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2013 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.795→50 Å / Num. all: 31761 / Num. obs: 31761 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 66.4 Å2 |
Reflection shell | Resolution: 2.795→2.9 Å / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entries 4KOL and 4DN3 Resolution: 2.795→48.405 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 33.46 / 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: 2.795→48.405 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Origin x: 55.7892 Å / Origin y: -16.1559 Å / Origin z: -21.1885 Å
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Refinement TLS group | Selection details: all |