6DC5

RSV prefusion F in complex with AM22 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.217 

Starting Models: experimental
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This is version 1.5 of the entry. See complete history


Literature

Alternative conformations of a major antigenic site on RSV F.

Jones, H.G.Battles, M.B.Lin, C.C.Bianchi, S.Corti, D.McLellan, J.S.

(2019) PLoS Pathog 15: e1007944-e1007944

  • DOI: https://doi.org/10.1371/journal.ppat.1007944
  • Primary Citation of Related Structures:  
    6DC3, 6DC4, 6DC5

  • PubMed Abstract: 

    The respiratory syncytial virus (RSV) fusion (F) glycoprotein is a major target of neutralizing antibodies arising from natural infection, and antibodies that specifically bind to the prefusion conformation of RSV F generally demonstrate the greatest neutralization potency. Prefusion-stabilized RSV F variants have been engineered as vaccine antigens, but crystal structures of these variants have revealed conformational differences in a key antigenic site located at the apex of the trimer, referred to as antigenic site Ø. Currently, it is unclear if flexibility in this region is an inherent property of prefusion RSV F or if it is related to inadequate stabilization of site Ø in the engineered variants. Therefore, we set out to investigate the conformational flexibility of antigenic site Ø, as well as the ability of the human immune system to recognize alternative conformations of this site, by determining crystal structures of prefusion RSV F bound to neutralizing human-derived antibodies AM22 and RSD5. Both antibodies bound with high affinity and were specific for the prefusion conformation of RSV F. Crystal structures of the complexes revealed that the antibodies recognized distinct conformations of antigenic site Ø, each diverging at a conserved proline residue located in the middle of an α-helix. These data suggest that antigenic site Ø exists as an ensemble of conformations, with individual antibodies recognizing discrete states. Collectively, these results have implications for the refolding of pneumovirus and paramyxovirus fusion proteins and should inform development of prefusion-stabilized RSV F vaccine candidates.


  • Organizational Affiliation

    Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RSV fusion glycoproteinA,
B [auth D],
C [auth G]
568Human respiratory syncytial virus A2Human immunodeficiency virus 1Mutation(s): 7 
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 GroupsM1E1E4P03420
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab AM22 heavy chainD [auth B],
F [auth E],
H
228Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q6GMX6 (Homo sapiens)
Explore Q6GMX6 
Go to UniProtKB:  Q6GMX6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6GMX6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab AM22 light chainE [auth C],
G [auth F],
I
215Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q8TCD0 (Homo sapiens)
Explore Q8TCD0 
Go to UniProtKB:  Q8TCD0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TCD0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
J [auth A],
L [auth D],
N [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CD
Query on CD

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K [auth A],
M [auth D],
O [auth G]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
P [auth C]
Q [auth C]
R [auth F]
S [auth F]
T [auth I]
P [auth C],
Q [auth C],
R [auth F],
S [auth F],
T [auth I],
U [auth I]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.217 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.45α = 90
b = 152.18β = 90
c = 202.93γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP20GM113132

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.2: 2020-01-22
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-10-16
    Changes: Structure summary