6OZ9 | pdb_00006oz9

Ebola virus glycoprotein in complex with EBOV-520 Fab

• PDB DOI: https://doi.org/10.2210/pdb6OZ9/pdb

• Classification: VIRAL PROTEIN/Immune system
• Organism(s): Ebola virus, Homo sapiens
• Expression System: Drosophila melanogaster, Homo sapiens
• Mutation(s): No 


• Deposited: 2019-05-15 Released: 2020-03-11 
• Deposition Author(s): Milligan, J.C., Altman, P.X., Hui, S., Hastie, K.M., Gilchuk, P., Crowe, J.E., 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: 3.46 Å
• R-Value Free: 
  0.234 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Analysis of a Therapeutic Antibody Cocktail Reveals Determinants for Cooperative and Broad Ebolavirus Neutralization.

Gilchuk, P., Murin, C.D., Milligan, J.C., Cross, R.W., Mire, C.E., Ilinykh, P.A., Huang, K., Kuzmina, N., Altman, P.X., Hui, S., Gunn, B.M., Bryan, A.L., Davidson, E., Doranz, B.J., Turner, H.L., Alkutkar, T., Flinko, R., Orlandi, C., Carnahan, R., Nargi, R., Bombardi, R.G., Vodzak, M.E., Li, S., Okoli, A., Ibeawuchi, M., Ohiaeri, B., Lewis, G.K., Alter, G., Bukreyev, A., Saphire, E.O., Geisbert, T.W., Ward, A.B., Crowe Jr., J.E.

(2020) Immunity 52: 388-403.e12

• PubMed: 32023489 
• DOI: https://doi.org/10.1016/j.immuni.2020.01.001
• Primary Citation Related Structures: 
  6OZ9, 6PCI, 6UYE


• PubMed Abstract: 
  

  Structural principles underlying the composition of protective antiviral monoclonal antibody (mAb) cocktails are poorly defined. Here, we exploited antibody cooperativity to develop a therapeutic mAb cocktail against Ebola virus. We systematically analyzed the antibody repertoire in human survivors and identified a pair of potently neutralizing mAbs that cooperatively bound to the ebolavirus glycoprotein (GP). High-resolution structures revealed that in a two-antibody cocktail, molecular mimicry was a major feature of mAb-GP interactions. Broadly neutralizing mAb rEBOV-520 targeted a conserved epitope on the GP base region. mAb rEBOV-548 bound to a glycan cap epitope, possessed neutralizing and Fc-mediated effector function activities, and potentiated neutralization by rEBOV-520. Remodeling of the glycan cap structures by the cocktail enabled enhanced GP binding and virus neutralization. The cocktail demonstrated resistance to virus escape and protected non-human primates (NHPs) against Ebola virus disease. These data illuminate structural principles of antibody cooperativity with implications for development of antiviral immunotherapeutics.

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Organizational Affiliation: 
• Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Galveston National Laboratory, Galveston, TX 77550, USA; Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.
Galveston National Laboratory, Galveston, TX 77550, USA; Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA.
Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.
Integral Molecular, Inc., Philadelphia, PA 19104, USA.
Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
Department of Medicine, University of California, San Diego, San Diego, CA 92093, USA.
First Consultants Medical Center, Lagos, Nigeria.
Galveston National Laboratory, Galveston, TX 77550, USA; Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA.
Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A3B3C3D3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 78.03 kDa 
• Atom Count: 5,408 
• Modeled Residue Count: 708 
• Deposited Residue Count: 713 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Small secreted glycoprotein sGP	A	158	Ebola virus	Mutation(s): 0  Gene Names:  sGP, DF49_53415gpsGP, DF49_53416gpsGP, DF49_53417gpsGP, DF49_53418gpsGP, DF49_53419gpsGP, DF49_53420gpsGP, DF49_53421gpsGP, DF49_53422gpsGP, DF49_53423gpsGP, DF49_53424gpsGP, DF49_53425gpsGP, DF49_53426gpsGP, DH33_45401gpsGP, DH33_45402gpsGP
UniProt
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76)) Explore Q05320  Go to UniProtKB:  Q05320

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein	B	113	Ebola virus	Mutation(s): 0  Gene Names: GP, DH33_45401gpGP
UniProt
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76)) Explore Q05320  Go to UniProtKB:  Q05320
Glycosylation
Glycosylation Sites: 1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
EBOV-520 Fab light chain	C [auth L]	215	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
EBOV-520 Fab heavy chain	D [auth H]	227	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.46 Å
• R-Value Free:  0.234 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 217.97	α = 90
b = 217.97	β = 90
c = 217.97	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: 2020-03-11 
Deposition Author(s): Milligan, J.C., Altman, P.X., Hui, S., Hastie, K.M., Gilchuk, P., Crowe, J.E., 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	U19 109762
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI132204
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	5T32AI007354-27

Revision History  

• Version 1.0: 2020-03-11
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-10-23
  Changes: Data collection, Database references, Structure summary