6DG2 | pdb_00006dg2

Antigen Binding Fragment of the Pan-ebolavirus Monoclonal Antibody 6D6

• PDB DOI: https://doi.org/10.2210/pdb6DG2/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2018-05-16 Released: 2018-09-26 
• Deposition Author(s): Milligan, J.C., Saphire, E.O.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.235 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Structural Characterization of Pan-Ebolavirus Antibody 6D6 Targeting the Fusion Peptide of the Surface Glycoprotein.

Milligan, J.C., Parekh, D.V., Fuller, K.M., Igarashi, M., Takada, A., Saphire, E.O.

(2019) J Infect Dis 219: 415-419

• PubMed: 30203042 
• DOI: https://doi.org/10.1093/infdis/jiy532
• Primary Citation Related Structures: 
  6DG2


• PubMed Abstract: 
  

  Ebola virus infection causes severe disease in humans and represents a global health threat. Candidates for immunotherapeutics and vaccines have shown promise in clinical trials, although they are ineffective against other members of the Ebolavirus genus that also cause periodic, lethal outbreaks. In this study, we present a crystal structure of a pan-ebolavirus antibody, 6D6, as well as single-particle electron microscopy reconstructions of 6D6 in complex with Ebola and Bundibugyo virus glycoproteins. 6D6 binds to the conserved glycoprotein fusion peptide, implicating it as a site of immune vulnerability that could be exploited to reliably elicit a pan-ebolavirus neutralizing antibody response.

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Organizational Affiliation: 
• Department of Immunology and Microbiology, La Jolla, California.
Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.
Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 96.76 kDa 
• Atom Count: 6,846 
• Modeled Residue Count: 851 
• Deposited Residue Count: 890 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6D6 Fab heavy chain	A, C	230	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
6D6 Fab light chain	B, D	215	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.235 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.226	α = 90
b = 72.038	β = 104.2
c = 107.149	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-09-26 
Deposition Author(s): Milligan, J.C., Saphire, E.O.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	5U19AI109762-05

Revision History  

• Version 1.0: 2018-09-26
  Type: Initial release
  
• Version 1.1: 2019-01-23
  Changes: Data collection, Database references
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary