[English] 日本語
Yorodumi- PDB-5yax: Crystal structure of a human neutralizing antibody bound to a HBV... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yax | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a human neutralizing antibody bound to a HBV preS1 peptide | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / HBV / NTCP / preS1 / antibody / Fc receptor | ||||||
Function / homology | Function and homology information caveolin-mediated endocytosis of virus by host cell / membrane => GO:0016020 / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Hepatitis B virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Liu, X. / Zheng, S. / Ye, K. / Sui, J. | ||||||
Citation | Journal: Elife / Year: 2017 Title: A potent human neutralizing antibody Fc-dependently reduces established HBV infections Authors: Li, D. / He, W. / Liu, X. / Zheng, S. / Qi, Y. / Li, H. / Mao, F. / Liu, J. / Sun, Y. / Pan, L. / Du, K. / Ye, K. / Li, W. / Sui, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5yax.cif.gz | 101.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5yax.ent.gz | 80.9 KB | Display | PDB format |
PDBx/mmJSON format | 5yax.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ya/5yax ftp://data.pdbj.org/pub/pdb/validation_reports/ya/5yax | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Antibody | Mass: 25737.184 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: scFv / Production host: Escherichia coli (E. coli) #2: Protein | | Mass: 6520.975 Da / Num. of mol.: 1 / Fragment: PreS1 peptide, UNP residues 2-59 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis B virus / Strain: isolate S472-20 / Production host: Escherichia coli (E. coli) / References: UniProt: B2CXZ0 #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.98 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 26, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 19392 / % possible obs: 96 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.144 / Χ2: 1.656 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 886 / Χ2: 1.114 / % possible all: 94.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.5→19.923 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.23 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→19.923 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|