Structure of IDP95734

Crystal structure of ZIKV-116 Fab in complex with ZIKV envelope DIII

(tree view)
Edit deposit information
CSGID target
IDP95734 
PDB Id
6PLK (NCBI MMDB) 
Authors
Zhao, H., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID) 
Responsible person
Chris Nelson 
Responsible lab
Washington University 
Deposition Date
Jul 01, 2019 
Release Date
Jul 11, 2019 

Annotation

Edit this annotation
Description
The antibody ZIKV-116 interferes with ZIKV infection at a post-cellular attachment step by blocking viral fusion with host membranes. ZIKV-116 recognizes the lateral ridge of envelope protein domain III (DIII), with one critical residue varying between the Asian and African strains responsible for differential binding affinity and neutralization potency (E393D). ZIKV-116 also binds to and cross-neutralizes some dengue virus serotype 1 strains, with genotype-dependent inhibition explained by variation in a domain II residue (R204K) that potentially modulates exposure of a distally located, partially cryptic epitope. 
Functional assignment
viral entry 

Ligands

Ligand code Name Ligand type

Structure information

View structure information | Edit structure information (upload a PDB file)

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=72.81Å, b=89.81Å, c=92.49Å
α=90.00, β=103.96, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
44.90-2.30Å (2.34-2.30Å)  
Rall(%)
17.0 
Rwork(%)
16.8 (2560.0) 
Rfree(%)
21.3 (2940.0) 
Num. observed reflections
52544 (2471) 
Num. Rfree reflections
2653 (0) 
Completeness(%)
97.2 (94.4) 

Model parameters

Num Atoms
8234  
Num Waters
401  
Num Hetatoms
401  
Model mean isotropic B factor
45.000Å2  
RMSD bond length
0.004Å  
RMSD bond angle
0.660°  
Filename uploaded
z116_refine_29.pdb (uploaded on Aug 31, 2020 12:47 PM)  
Inserted
Aug 31, 2020