7KEX

Ebola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-293


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Convergence of a common solution for broad ebolavirus neutralization by glycan cap-directed human antibodies.

Murin, C.D.Gilchuk, P.Ilinykh, P.A.Huang, K.Kuzmina, N.Shen, X.Bruhn, J.F.Bryan, A.L.Davidson, E.Doranz, B.J.Williamson, L.E.Copps, J.Alkutkar, T.Flyak, A.I.Bukreyev, A.Crowe Jr., J.E.Ward, A.B.

(2021) Cell Rep 35: 108984-108984

  • DOI: 10.1016/j.celrep.2021.108984
  • Primary Citation of Related Structures:  
    7KFE, 7KFB, 7KFH, 7KFG, 7KEW, 7KEX, 7KF9

  • PubMed Abstract: 
  • Antibodies that target the glycan cap epitope on the ebolavirus glycoprotein (GP) are common in the adaptive response of survivors. A subset is known to be broadly neutralizing, but the details of their epitopes and basis for neutralization are not well understood ...

    Antibodies that target the glycan cap epitope on the ebolavirus glycoprotein (GP) are common in the adaptive response of survivors. A subset is known to be broadly neutralizing, but the details of their epitopes and basis for neutralization are not well understood. Here, we present cryoelectron microscopy (cryo-EM) structures of diverse glycan cap antibodies that variably synergize with GP base-binding antibodies. These structures describe a conserved site of vulnerability that anchors the mucin-like domains (MLDs) to the glycan cap, which we call the MLD anchor and cradle. Antibodies that bind to the MLD cradle share common features, including use of IGHV1-69 and IGHJ6 germline genes, which exploit hydrophobic residues and form β-hairpin structures to mimic the MLD anchor, disrupt MLD attachment, destabilize GP quaternary structure, and block cleavage events required for receptor binding. Our results provide a molecular basis for ebolavirus neutralization by broadly reactive glycan cap antibodies.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: andrew@scripps.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody Fab EBOV-293 light chainA [auth J], E [auth K], I [auth L]232Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody Fab EBOV-293 heavy chainB [auth G], F [auth H], J [auth I]244Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Virion spike glycoprotein 1C [auth A], G [auth B], K [auth C]313Ebola virusMutation(s): 0 
Gene Names: GP
Find proteins for A0A1C4HDV6 (Ebola virus)
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Go to UniProtKB:  A0A1C4HDV6
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Virion spike glycoprotein 2D, H [auth E], L [auth F]203Ebola virusMutation(s): 0 
Find proteins for A0A0E3XK95 (Zaire ebolavirus)
Explore A0A0E3XK95 
Go to UniProtKB:  A0A0E3XK95
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Oligosaccharides

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Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseM, O, Q3 N-Glycosylation Oligosaccharides Interaction
Entity ID: 6
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
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-glucopyranoseN, P, R4 N-Glycosylation Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU19 AI142785

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-28
    Type: Initial release