6OUS

Structure of fusion glycoprotein from human respiratory syncytial virus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.245 

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Literature

A potent broadly neutralizing human RSV antibody targets conserved site IV of the fusion glycoprotein.

Tang, A., Chen, Z., Cox, K.S., Su, H.P., Callahan, C., Fridman, A., Zhang, L., Patel, S.B., Cejas, P.J., Swoyer, R., Touch, S., Citron, M.P., Govindarajan, D., Luo, B., Eddins, M., Reid, J.C., Soisson, S.M., Galli, J., Wang, D., Wen, Z., Heidecker, G.J., Casimiro, D.R., DiStefano, D.J., Vora, K.A.

(2019) Nat Commun 10: 4153-4153

  • DOI: https://doi.org/10.1038/s41467-019-12137-1
  • Primary Citation of Related Structures:  
    6OUS

  • PubMed Abstract: 

    • Respiratory syncytial virus (RSV) infection is the leading cause of hospitalization and infant mortality under six months of age worldwide; therefore, the prevention of RSV infection in all infants represents a significant unmet medical need. Here we report the isolation of a potent and broadly neutralizing RSV monoclonal antibody derived from a human memory B-cell ...

    Respiratory syncytial virus (RSV) infection is the leading cause of hospitalization and infant mortality under six months of age worldwide; therefore, the prevention of RSV infection in all infants represents a significant unmet medical need. Here we report the isolation of a potent and broadly neutralizing RSV monoclonal antibody derived from a human memory B-cell. This antibody, RB1, is equipotent on RSV A and B subtypes, potently neutralizes a diverse panel of clinical isolates in vitro and demonstrates in vivo protection. It binds to a highly conserved epitope in antigenic site IV of the RSV fusion glycoprotein. RB1 is the parental antibody to MK-1654 which is currently in clinical development for the prevention of RSV infection in infants.

    Organizational Affiliation: 

    Department of Infectious Diseases and Vaccines Research, Merck & Co., Inc, West Point, PA, USA. kalpit.vora@merck.com.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fusion glycoprotein F2
A, C, E, G, I
A, C, E, G, I, K
84Human respiratory syncytial virus A2Mutation(s): 0 
Gene Names: F
UniProt
Find proteins for P03420 (Human respiratory syncytial virus A (strain A2))
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Go to UniProtKB:  P03420
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03420
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fusion glycoprotein F1 fused with Fibritin trimerization domain
B, D, F, H, J
B, D, F, H, J, L
414Human respiratory syncytial virus A2, Human immunodeficiency virus 1
This entity is chimeric		Mutation(s): 0 
Gene Names: F
UniProt
Find proteins for M1E1E4 (Human immunodeficiency virus 1)
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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
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RB1 Fab Heavy Chain
M, O, Q, S, U
M, O, Q, S, U, W
231Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RB1 Fab Light chain
N, P, R, T, V
N, P, R, T, V, X
214Homo sapiensMutation(s): 0 
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Oligosaccharides

Help

Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
BA [auth b],
CA [auth c],
DA [auth d],
Y,
AA [auth a],
BA [auth b],
CA [auth c],
DA [auth d],
Y,
Z
4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
EA [auth B],
FA [auth F],
GA [auth J],
HA [auth L]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A, C, E, G, I
A, C, E, G, I, K
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.245 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.153α = 87.24
b = 126.595β = 79.15
c = 148.165γ = 86.29
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2019-10-30 
    • Deposition Author(s): Su, H.P.

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-30
    Type: Initial release
  • Version 2.0: 2019-12-25
    Changes: Database references, Polymer sequence
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary