[English] 日本語
Yorodumi- PDB-4wht: Structure of the Hepatitis C virus envelope glycoprotein E2 antig... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wht | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423 bound to the broadly neutralizing antibody 3/11, P1 crystal form | ||||||
Components |
| ||||||
Keywords | VIRAL PROTEIN / neutralizing epitope / envelope glycoprotein / E2 / receptor-binding | ||||||
Function / homology | Function and homology information host cell lipid droplet / lipid droplet / clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / viral envelope / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Hepatitis C virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.22 Å | ||||||
Authors | Krey, T. / Rey, F.A. | ||||||
Funding support | France, 1items
| ||||||
Citation | Journal: J.Virol. / Year: 2015 Title: Structural flexibility of a conserved antigenic region in hepatitis C virus glycoprotein e2 recognized by broadly neutralizing antibodies. Authors: Meola, A. / Tarr, A.W. / England, P. / Meredith, L.W. / McClure, C.P. / Foung, S.K. / McKeating, J.A. / Ball, J.K. / Rey, F.A. / Krey, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4wht.cif.gz | 968.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4wht.ent.gz | 820.1 KB | Display | PDB format |
PDBx/mmJSON format | 4wht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wht_validation.pdf.gz | 637.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4wht_full_validation.pdf.gz | 678.9 KB | Display | |
Data in XML | 4wht_validation.xml.gz | 167.8 KB | Display | |
Data in CIF | 4wht_validation.cif.gz | 235 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/4wht ftp://data.pdbj.org/pub/pdb/validation_reports/wh/4wht | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
6 |
| ||||||||
7 |
| ||||||||
8 |
| ||||||||
9 |
| ||||||||
10 |
| ||||||||
11 |
| ||||||||
12 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological unit is a heterotrimer containing heavy and light chain of the Fab fragment and one synthetic peptide. There are 12 biological units in the asymmetric unit (chains A&B+a, chains C&D+c, chains E&F+e, chains G&H+g, chains I&J+i, chains K&L+k, chains M&N+m, chains O&P+o, chains Q&R+q, chains S&T+s, chains U&V+u, chains X&Y+x). |
-Components
#1: Antibody | Mass: 26893.855 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pMT/BiP based / Cell line (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly) #2: Antibody | Mass: 23909.492 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly) #3: Protein/peptide | Mass: 1383.489 Da / Num. of mol.: 12 / Fragment: UNP residues 51-62 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus / Production host: synthetic construct (others) / References: UniProt: Q9WJJ4 #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.84 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM TRIS, 27% PEG4000, 100mM Na-Acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97902 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97902 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→48.74 Å / Num. obs: 246066 / % possible obs: 95.4 % / Redundancy: 2.4 % / Biso Wilson estimate: 39.67 Å2 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.22→2.34 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 1.8 / % possible all: 81.4 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→32.5 Å / Cor.coef. Fo:Fc: 0.8968 / Cor.coef. Fo:Fc free: 0.8698 / SU R Cruickshank DPI: 0.322 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.298 / SU Rfree Blow DPI: 0.213 / SU Rfree Cruickshank DPI: 0.221
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 141.01 Å2 / Biso mean: 41.72 Å2 / Biso min: 8.07 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.325 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.22→32.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.22→2.28 Å / Total num. of bins used: 20
|