6OTC

Synthetic Fab bound to Marburg virus VP35 interferon inhibitory domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inhibition of Marburg Virus RNA Synthesis by a Synthetic Anti-VP35 Antibody.

Amatya, P.Wagner, N.Chen, G.Luthra, P.Shi, L.Borek, D.Pavlenco, A.Rohrs, H.Basler, C.F.Sidhu, S.S.Gross, M.L.Leung, D.W.

(2019) Acs Infect Dis. 5: 1385-1396

  • DOI: 10.1021/acsinfecdis.9b00091

  • PubMed Abstract: 
  • Marburg virus causes sporadic outbreaks of severe hemorrhagic fever with high case fatality rates. Approved, effective, and safe therapeutic or prophylactic countermeasures are lacking. To address this, we used phage display to engineer a synthetic a ...

    Marburg virus causes sporadic outbreaks of severe hemorrhagic fever with high case fatality rates. Approved, effective, and safe therapeutic or prophylactic countermeasures are lacking. To address this, we used phage display to engineer a synthetic antibody, sFab H3, which binds the Marburg virus VP35 protein (mVP35). mVP35 is a critical cofactor of the viral replication complex and a viral immune antagonist. sFab H3 displayed high specificity for mVP35 and not for the closely related Ebola virus VP35. sFab H3 inhibited viral RNA synthesis in a minigenome assay, suggesting its potential use as an antiviral. We characterized sFab H3 by a combination of biophysical and biochemical methods, and a crystal structure of the complex solved to 1.7 Å resolution defined the molecular interface between sFab H3 and mVP35 interferon inhibitory domain. Our study identifies mVP35 as a therapeutic target using an approach that provides a framework for generating engineered Fabs targeting other viral proteins.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polymerase cofactor VP35
A
129Lake Victoria marburgvirus (strain Popp-67)Mutation(s): 0 
Gene Names: VP35
Find proteins for Q03039 (Lake Victoria marburgvirus (strain Popp-67))
Go to UniProtKB:  Q03039
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
sFab H3 heavy chain
H
240N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
sFab H3 light chain
L
232N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
H
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.827α = 90.00
b = 97.422β = 90.00
c = 110.325γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesP01AI120943
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01AI140758
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP41GM103422

Revision History 

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-07-10
    Type: Data collection, Database references
  • Version 1.2: 2019-08-21
    Type: Data collection, Database references