[English] 日本語
Yorodumi- PDB-6ivz: Crystal structure of 5A ScFv complexed with YFV-China sE in postf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ivz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of 5A ScFv complexed with YFV-China sE in postfusion state | ||||||
Components |
| ||||||
Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / Yellow fever virus / Neutralizing monoclonal antibody / Envelope protein / Flavivirus / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Yellow fever virus Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å | ||||||
Authors | Lu, X.S. / Xiao, H.X. / Li, S.H. / Pang, X.F. | ||||||
Citation | Journal: Cell Rep / Year: 2019 Title: Double Lock of a Human Neutralizing and Protective Monoclonal Antibody Targeting the Yellow Fever Virus Envelope. Authors: Lu, X. / Xiao, H. / Li, S. / Pang, X. / Song, J. / Liu, S. / Cheng, H. / Li, Y. / Wang, X. / Huang, C. / Guo, T. / Ter Meulen, J. / Daffis, S. / Yan, J. / Dai, L. / Rao, Z. / Klenk, H.D. / ...Authors: Lu, X. / Xiao, H. / Li, S. / Pang, X. / Song, J. / Liu, S. / Cheng, H. / Li, Y. / Wang, X. / Huang, C. / Guo, T. / Ter Meulen, J. / Daffis, S. / Yan, J. / Dai, L. / Rao, Z. / Klenk, H.D. / Qi, J. / Shi, Y. / Gao, G.F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ivz.cif.gz | 248 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ivz.ent.gz | 206.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ivz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ivz_validation.pdf.gz | 436.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6ivz_full_validation.pdf.gz | 442.4 KB | Display | |
Data in XML | 6ivz_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 6ivz_validation.cif.gz | 34.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/6ivz ftp://data.pdbj.org/pub/pdb/validation_reports/iv/6ivz | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 42950.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yellow fever virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q89292 |
---|---|
#2: Antibody | Mass: 13674.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
#3: Antibody | Mass: 13391.690 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.68 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 0.1 M Sodium malonate pH 4.0, 12% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 25919 / % possible obs: 99.9 % / Redundancy: 14.6 % / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 2.4→50 Å |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.4→47.391 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.24
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→47.391 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|