[English] 日本語
Yorodumi- PDB-6gg0: Cryo-EM structure of BK polyomavirus like particle in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gg0 | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of BK polyomavirus like particle in complex with single chain antibody ScFv41F17 | ||||||
Components |
| ||||||
Keywords | VIRUS LIKE PARTICLE / BK polyoma virus / Single chain antibody / cross neutralizing antibody | ||||||
Function / homology | Function and homology information caveolin-mediated endocytosis of virus by host cell / T=7 icosahedral viral capsid / host cell nucleus / virion attachment to host cell / structural molecule activity Similarity search - Function | ||||||
Biological species | BK polyomavirus Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.24 Å | ||||||
Authors | Srinivas, H. | ||||||
Citation | Journal: Immunity / Year: 2019 Title: Human Memory B Cells Harbor Diverse Cross-Neutralizing Antibodies against BK and JC Polyomaviruses. Authors: John M Lindner / Vanessa Cornacchione / Atul Sathe / Celine Be / Honnappa Srinivas / Elodie Riquet / Xavier-Charles Leber / Andreas Hein / Matthias B Wrobel / Meike Scharenberg / Thomas ...Authors: John M Lindner / Vanessa Cornacchione / Atul Sathe / Celine Be / Honnappa Srinivas / Elodie Riquet / Xavier-Charles Leber / Andreas Hein / Matthias B Wrobel / Meike Scharenberg / Thomas Pietzonka / Christian Wiesmann / Johanna Abend / Elisabetta Traggiai / Abstract: Human polyomaviruses cause a common childhood infection worldwide and typically elicit a neutralizing antibody and cellular immune response, while establishing a dormant infection in the kidney with ...Human polyomaviruses cause a common childhood infection worldwide and typically elicit a neutralizing antibody and cellular immune response, while establishing a dormant infection in the kidney with minimal clinical manifestations. However, viral reactivation can cause severe pathology in immunocompromised individuals. We developed a high-throughput, functional antibody screen to examine the humoral response to BK polyomavirus. This approach enabled the isolation of antibodies from all peripheral B cell subsets and revealed the anti-BK virus antibody repertoire as clonally complex with respect to immunoglobulin sequences and isotypes (both IgM and IgG), including a high frequency of monoclonal antibodies that broadly neutralize BK virus subtypes and the related JC polyomavirus. Cryo-electron microscopy of a broadly neutralizing IgG single-chain variable fragment complexed with BK virus-like particles revealed the quaternary nature of a conserved viral epitope at the junction between capsid pentamers. These features unravel a potent modality for inhibiting polyomavirus infection in kidney transplant recipients and other immunocompromised patients. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6gg0.cif.gz | 386.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6gg0.ent.gz | 327.7 KB | Display | PDB format |
PDBx/mmJSON format | 6gg0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gg0_validation.pdf.gz | 874.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6gg0_full_validation.pdf.gz | 908.2 KB | Display | |
Data in XML | 6gg0_validation.xml.gz | 75.1 KB | Display | |
Data in CIF | 6gg0_validation.cif.gz | 112.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/6gg0 ftp://data.pdbj.org/pub/pdb/validation_reports/gg/6gg0 | HTTPS FTP |
-Related structure data
Related structure data | 4398MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
| x 60
2 |
|
3 |
| x 5
4 |
| x 6
5 |
|
Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 40184.641 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BK polyomavirus / Gene: VP1, vp1, BK1035_00004, BK1055_00004 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q65613, UniProt: P03088*PLUS #2: Antibody | | Mass: 13339.808 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: 11719.086 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) |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 13.8 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
| ||||||||||||||||||||||||
Source (recombinant) |
| ||||||||||||||||||||||||
Buffer solution | pH: 8 / Details: 25mM Tris-HCl pH8.0 100mM NaCl | ||||||||||||||||||||||||
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER |
Image recording | Electron dose: 1.1 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: NONE | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 10000 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6000 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|