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 6CXC | pdb_00006cxc

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

Validation slider image for 6CXC

This is version 1.4 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: https://doi.org/10.1371/journal.pone.0210749
  • Primary Citation 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. 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: 
    • Department of Bioengineering, Rice University, Houston, Texas, United States of America.

Macromolecule Content 

  • Total Structure Weight: 444.56 kDa 
  • Atom Count: 15,196 
  • Modeled Residue Count: 1,945 
  • Deposited Residue Count: 4,008 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
R4.C6 Fab Heavy ChainA [auth X],
C [auth G],
E [auth I]
118Mus musculusMutation(s): 0 
Entity Groups
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
R4.C6 Fab Light ChainB [auth Y],
D [auth J],
F [auth K]
122Mus musculusMutation(s): 0 
Entity Groups
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Fusion glycoprotein F0, Envelope glycoprotein chimera548Human respiratory syncytial virus A2, Human immunodeficiency virus 1
This entity is chimeric
Mutation(s): 0 
UniProt
Find proteins for M1E1E4 (Human immunodeficiency virus type 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
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UniProt GroupsP03420M1E1E4
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.0
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



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
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Structure summary
  • Version 1.4: 2025-06-04
    Changes: Data collection