6PCI

EBOV GPdMuc (Makona) in complex with rEBOV-520 and rEBOV-548 Fabs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1016/j.immuni.2020.01.001
  • Primary Citation of 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.


  • Organizational Affiliation

    Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Virion spike glycoproteinA,
G [auth B],
M [auth C]
278Ebola virusMutation(s): 0 
Gene Names: GP
UniProt
Find proteins for A0A068J419 (Zaire ebolavirus)
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Go to UniProtKB:  A0A068J419
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A068J419
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
rEBOV-548 Fab heavy chainB [auth H],
H [auth I],
N [auth J]
234Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
rEBOV-548 Fab light chainC [auth K],
I [auth L],
O [auth M]
214Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Virion spike glycoprotein,Virion spike glycoprotein,Ebola Virus (Makona) GP2D,
J [auth E],
P [auth F]
203Zaire ebolavirusEbola virus
This entity is chimeric
Mutation(s): 0 
Gene Names: GP
UniProt
Find proteins for A0A068J419 (Zaire ebolavirus)
Explore A0A068J419 
Go to UniProtKB:  A0A068J419
Entity Groups  
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UniProt GroupA0A068J419
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
rEBOV-520 Fab light chainE [auth Q],
K [auth R],
Q [auth S]
215Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
rEBOV-520 Fab heavy chainF [auth N],
L [auth O],
R [auth P]
227Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
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-glucopyranoseS [auth G],
T,
U
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth C]
EA [auth C]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth C],
EA [auth C],
FA [auth C],
GA [auth C],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTRosetta
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU19 AI109762

Revision History  (Full details and data files)

  • 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: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary