Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 12-mer - A3B3C3D3 Pseudo Symmetry: Cyclic - C3  (3D View)
Pseudo Stoichiometry: Hetero 12-mer - A6B3C3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 240.89 kDa 
• Atom Count: 12693 
• Residue Count: 1587 
• Unique protein chains: 4

6DZL

Ebola virus Makona variant GP (mucin-deleted) in complex with pan-ebolavirus human antibody ADI-15878 Fab

• DOI: 10.2210/pdb6DZL/pdb
• EMDataResource: EMD-8935

• Classification: VIRAL PROTEIN
• Organism(s): Ebola virus - Zaire (1995), Homo sapiens
• Expression System: Homo sapiens, Nicotiana benthamiana
• Mutation(s): No 


• Deposited: 2018-07-05 Released: 2018-09-12 
• Deposition Author(s): Murin, C.D., Ward, A.B.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.14 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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: 10.1016/j.celrep.2018.08.009
• Primary Citation of Related Structures:  
  6DZM, 6DZL, 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. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ebola virus Makona GP1	A, B, C	321	Ebola virus - Zaire (1995)	Mutation(s): 0  Gene Names: GP
Find proteins for P87666 (Zaire ebolavirus (strain Kikwit-95)) Explore P87666  Go to UniProtKB:  P87666

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ebola virus Makona GP2	D, E, F	166	Ebola virus - Zaire (1995)	Mutation(s): 0  Gene Names: GP
Find proteins for P87666 (Zaire ebolavirus (strain Kikwit-95)) Explore P87666  Go to UniProtKB:  P87666

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fv domain of ADI-15878 Fab light chain	J, K, L	106	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fv domain of ADI-15878 Fab heavy chain	G, H, I	121	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M, O, Q	2		N-Glycosylation

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	N, P, R	6		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B, C	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.14 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-07-05 
• Released Date: 2018-09-12 
Deposition Author(s): Murin, C.D., Ward, A.B.

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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 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary