[English] 日本語
Yorodumi- EMDB-0916: Neutralization mechanism of a monoclonal antibody targeting a por... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0916 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Neutralization mechanism of a monoclonal antibody targeting a porcine circovirus type 2 Cap protein conformational epitope | |||||||||
Map data | 3D cry-EM map of PCV2 vision | |||||||||
Sample |
| |||||||||
Keywords | Porcine circovirus type 2 / Cap protein / VIRUS | |||||||||
Function / homology | Circovirus capsid protein / Circovirus capsid superfamily / Circovirus capsid protein / viral capsid assembly / T=1 icosahedral viral capsid / symbiont entry into host cell / virion attachment to host cell / Capsid protein Function and homology information | |||||||||
Biological species | Porcine circovirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.7 Å | |||||||||
Authors | Sun Z / Huang L | |||||||||
Funding support | China, 1 items
| |||||||||
Citation | Journal: J Virol / Year: 2020 Title: Neutralization Mechanism of a Monoclonal Antibody Targeting a Porcine Circovirus Type 2 Cap Protein Conformational Epitope. Authors: Liping Huang / Zhenzhao Sun / Deli Xia / Yanwu Wei / Encheng Sun / Chunguo Liu / Hongzhen Zhu / Haiqiao Bian / Hongli Wu / Li Feng / Jingfei Wang / Changming Liu / Abstract: Porcine circovirus type 2 (PCV2) is an important pathogen in swine herds, and its infection of pigs has caused severe economic losses to the pig industry worldwide. The capsid protein of PCV2 is the ...Porcine circovirus type 2 (PCV2) is an important pathogen in swine herds, and its infection of pigs has caused severe economic losses to the pig industry worldwide. The capsid protein of PCV2 is the only structural protein that is associated with PCV2 infection and immunity. Here, we report a neutralizing monoclonal antibody (MAb), MAb 3A5, that binds to intact PCV2 virions of the PCV2a, PCV2b, and PCV2d genotypes. MAb 3A5 neutralized PCV2 by blocking viral attachment to PK15 cells. To further explore the neutralization mechanism, we resolved the structure of the PCV2 virion in complex with MAb 3A5 Fab fragments by using cryo-electron microscopy single-particle analysis. The binding sites were located at the topmost edges around 5-fold icosahedral symmetry axes, with each footprint covering amino acids from two adjacent capsid proteins. Most of the epitope residues (15/18 residues) were conserved among 2,273 PCV2 strains. Mutations of some amino acids within the epitope had significant effects on the neutralizing activity of MAb 3A5. This study reveals the molecular and structural bases of this PCV2-neutralizing antibody and provides new and important information for vaccine design and therapeutic antibody development against PCV2 infections. PCV2 is associated with several clinical manifestations collectively known as PCV2-associated diseases (PCVADs). Neutralizing antibodies play a crucial role in the prevention of PCVADs. We demonstrated previously that a MAb, MAb 3A5, neutralizes the PCV2a, PCV2b, and PCV2d genotypes with different degrees of efficiency, but the underlying mechanism remains elusive. Here, we report the neutralization mechanism of this MAb and the structure of the PCV2 virion in complex with MAb 3A5 Fabs, showing a binding mode in which one Fab interacted with more than two loops from two adjacent capsid proteins. This binding mode has not been observed previously for PCV2-neutralizing antibodies. Our work provides new and important information for vaccine design and therapeutic antibody development against PCV2 infections. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0916.map.gz | 17.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-0916-v30.xml emd-0916.xml | 9.2 KB 9.2 KB | Display Display | EMDB header |
Images | emd_0916.png | 246.6 KB | ||
Filedesc metadata | emd-0916.cif.gz | 4.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0916 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0916 | HTTPS FTP |
-Validation report
Summary document | emd_0916_validation.pdf.gz | 453.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_0916_full_validation.pdf.gz | 452.8 KB | Display | |
Data in XML | emd_0916_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | emd_0916_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0916 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0916 | HTTPS FTP |
-Related structure data
Related structure data | 6lm3MC 0838C 6l62C M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_0916.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | 3D cry-EM map of PCV2 vision | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : PCV2 virion in complex with Fab fragments of the mAb 3A5
Entire | Name: PCV2 virion in complex with Fab fragments of the mAb 3A5 |
---|---|
Components |
|
-Supramolecule #1: PCV2 virion in complex with Fab fragments of the mAb 3A5
Supramolecule | Name: PCV2 virion in complex with Fab fragments of the mAb 3A5 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Porcine circovirus 2 |
-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Porcine circovirus 2 |
Molecular weight | Theoretical: 27.55952 KDa |
Recombinant expression | Organism: Porcine circovirus 2 |
Sequence | String: MTYPRRRFRR RRHRPRSHLG LILRRRPWLV HPRHRYRWRR KNGIFNTRLS CTFGYTVKAT TVRTPSWAVD MMRFNINDFV PPGGGTNKI SIPFEYYRIR KVKVEFWPCS PITQGDRGVG STAVILDDNF VTKATALTYD PYVNYSSRHT IPQPFSYHSR Y FTPKPVLD ...String: MTYPRRRFRR RRHRPRSHLG LILRRRPWLV HPRHRYRWRR KNGIFNTRLS CTFGYTVKAT TVRTPSWAVD MMRFNINDFV PPGGGTNKI SIPFEYYRIR KVKVEFWPCS PITQGDRGVG STAVILDDNF VTKATALTYD PYVNYSSRHT IPQPFSYHSR Y FTPKPVLD STIDYFQPNN KRNQLWLRLQ TSANVDHVGL GIAFENSTYD QDYNIRVTMY VQFREFNLKD PPL UniProtKB: Capsid protein |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
---|---|
Image recording | Film or detector model: FEI CETA (4k x 4k) / Average electron dose: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2011 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |