7KFE

Bundibugyo virus GP (mucin deleted) bound to antibody Fab BDBV-329


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.60 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 BDBV-329 heavy chainC [auth G], A [auth H]244Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody BDBV-329 light chainD [auth I], B [auth J]215Homo sapiensMutation(s): 0 
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoprotein 1E [auth A], G [auth B], I [auth C]343Bundibugyo ebolavirusMutation(s): 0 
Gene Names: GP
Find proteins for A0A510C2V9 (Bundibugyo ebolavirus)
Explore A0A510C2V9 
Go to UniProtKB:  A0A510C2V9
Protein Feature View
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein 2F [auth D], H [auth E], J [auth F]177Bundibugyo ebolavirusMutation(s): 0 
Gene Names: GPDF49_53413gpGPDH33_45404gpGP
Find proteins for B8XCN0 (Bundibugyo ebolavirus)
Explore B8XCN0 
Go to UniProtKB:  B8XCN0
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChainsChain 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-glucopyranoseK, M, O5 N-Glycosylation Oligosaccharides Interaction
Entity ID: 6
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseL, N2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
P [auth B], Q [auth C]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.60 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 States--

Revision History  (Full details and data files)

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