6DZN | pdb_00006dzn

Pan-ebolavirus human antibody ADI-15878 Fab

• PDB DOI: https://doi.org/10.2210/pdb6DZN/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2018-07-05 Released: 2018-09-12 
• Deposition Author(s): Murin, C.D., Ward, A.B., Bruhn, J.F., Stanfield, R.
• 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: 2.10 Å
• R-Value Free: 
  0.265 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Literature

Structural Basis of Pan-Ebolavirus Neutralization by an Antibody Targeting the Glycoprotein Fusion Loop.

Murin, C.D., Bruhn, J.F., Bornholdt, Z.A., Copps, J., Stanfield, R., Ward, A.B.

(2018) Cell Rep 24: 2723-2732.e4

• PubMed: 30184505 
• DOI: https://doi.org/10.1016/j.celrep.2018.08.009
• Primary Citation Related Structures: 
  6DZL, 6DZM, 6DZN


• PubMed Abstract: 
  

  Monoclonal antibodies (mAbs) with pan-ebolavirus cross-reactivity are highly desirable, but development of such mAbs is limited by a lack of a molecular understanding of cross-reactive epitopes. The antibody ADI-15878 was previously identified from a human survivor of Ebola virus Makona variant (EBOV/Mak) infection. This mAb demonstrated potent neutralizing activity against all known ebolaviruses and provided protection in rodent and ferret models against three ebolavirus species. Here, we describe the unliganded crystal structure of ADI-15878 as well as the cryo-EM structures of ADI-15878 in complex with the EBOV/Mak and Bundibugyo virus (BDBV) glycoproteins (GPs). ADI-15878 binds through an induced-fit mechanism by targeting highly conserved residues in the internal fusion loop (IFL), bridging across GP protomers via the heptad repeat 1 (HR1) region. Our structures provide a more complete description of the ebolavirus immunogenic landscape, as well as a molecular basis for how rare but potent antibodies target conserved filoviral fusion machinery.

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Organizational Affiliation: 
• Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Sciences, La Jolla, CA 92037, USA.
Mapp Biopharmaceutical, San Diego, CA 92121, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: [e-mail].

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

Macromolecule Content 

• Total Structure Weight: 47.66 kDa 
• Atom Count: 3,660 
• Modeled Residue Count: 439 
• Deposited Residue Count: 439 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody ADI-15878, light chain	A [auth L]	213	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody ADI-15878, heavy chain	B [auth H]	226	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	G [auth L]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
AE3	F [auth L]	2-(2-ETHOXYETHOXY)ETHANOL C6 H14 O3 XXJWXESWEXIICW-UHFFFAOYSA-N
CL	C [auth L], D [auth L], E [auth L], H, I [auth H], J [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.265 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.057	α = 90
b = 96.837	β = 102.91
c = 54.309	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-09-12 
Deposition Author(s): Murin, C.D., Ward, A.B., Bruhn, J.F., Stanfield, R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19 AI109762

Revision History  

• Version 1.0: 2018-09-12
  Type: Initial release
  
• Version 1.1: 2018-09-19
  Changes: Data collection, Database references
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Structure summary