6CXC

3.9A Cryo-EM structure of murine antibody bound at a novel epitope of respiratory syncytial virus fusion protein


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure basis of neutralization by a novel site II/IV antibody against respiratory syncytial virus fusion protein.

Xie, Q.Wang, Z.Ni, F.Chen, X.Ma, J.Patel, N.Lu, H.Liu, Y.Tian, J.H.Flyer, D.Massare, M.J.Ellingsworth, L.Glenn, G.Smith, G.Wang, Q.

(2019) PLoS One 14: e0210749-e0210749

  • DOI: 10.1371/journal.pone.0210749
  • Primary Citation of Related Structures:  
    6CXC

  • PubMed Abstract: 
  • Globally, human respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract infections in newborns, young children, and the elderly for which there is no vaccine. The RSV fusion (F) glycoprotein is a major target for vaccine development ...

    Globally, human respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract infections in newborns, young children, and the elderly for which there is no vaccine. The RSV fusion (F) glycoprotein is a major target for vaccine development. Here, we describe a novel monoclonal antibody (designated as R4.C6) that recognizes both pre-fusion and post-fusion RSV F, and binds with nanomole affinity to a unique neutralizing site comprised of antigenic sites II and IV on the globular head. A 3.9 Å-resolution structure of RSV F-R4.C6 Fab complex was obtained by single particle cryo-electron microscopy and 3D reconstruction. The structure unraveled detailed interactions of R4.C6 with antigenic site II on one protomer and site IV on a neighboring protomer of post-fusion RSV F protein. These findings significantly further our understanding of the antigenic complexity of the F protein and provide new insights into RSV vaccine design.


    Organizational Affiliation

    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
R4.C6 Fab Heavy ChainC [auth G],
E [auth I],
A [auth X]
118Mus musculusMutation(s): 0 
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Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
R4.C6 Fab Light ChainD [auth J],
F [auth K],
B [auth Y]
122Mus musculusMutation(s): 0 
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Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fusion glycoprotein F0, Envelope glycoprotein chimera548Human respiratory syncytial virus A2Human immunodeficiency virus 1
This entity is chimeric
Mutation(s): 0 
Gene Names: F
UniProt
Find proteins for M1E1E4 (Human immunodeficiency virus 1)
Explore M1E1E4 
Go to UniProtKB:  M1E1E4
Find proteins for P03420 (Human respiratory syncytial virus A (strain A2))
Explore P03420 
Go to UniProtKB:  P03420
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP03420M1E1E4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
M [auth A],
N [auth B],
O [auth C],
P [auth D],
Q [auth E],
M [auth A],
N [auth B],
O [auth C],
P [auth D],
Q [auth E],
R [auth F]
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: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2020-02-12
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary