5WNB | pdb_00005wnb

Structure of antibody 3D3 bound to the linear epitope of RSV G


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.268 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structures of respiratory syncytial virus G antigen bound to broadly neutralizing antibodies.

Fedechkin, S.O.George, N.L.Wolff, J.T.Kauvar, L.M.DuBois, R.M.

(2018) Sci Immunol 3

  • DOI: https://doi.org/10.1126/sciimmunol.aar3534
  • Primary Citation Related Structures: 
    5WN9, 5WNA, 5WNB

  • PubMed Abstract: 

    Respiratory syncytial virus (RSV) is a top cause of severe lower respiratory tract disease and mortality in young children and the elderly. The viral envelope G glycoprotein contributes to pathogenesis through its roles in host cell attachment and modulation of host immunity. Although the G glycoprotein is a target of protective RSV-neutralizing antibodies, its development as a vaccine antigen has been hindered by its heterogeneous glycosylation and sequence variability outside a conserved central domain (CCD). We describe the cocrystal structures of two high-affinity broadly neutralizing human monoclonal antibodies bound to the RSV G CCD. The antibodies bind to neighboring conformational epitopes, which we named antigenic sites γ1 and γ2, that span a highly conserved surface, illuminating an important region of vulnerability. We further show that isolated RSV G CCD activates the chemokine receptor CX3CR1 and that antibodies block this activity. These studies provide a template for rational vaccine design targeting this key contributor to RSV disease.


  • Organizational Affiliation
    • Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.

Macromolecule Content 

  • Total Structure Weight: 100.36 kDa 
  • Atom Count: 6,664 
  • Modeled Residue Count: 877 
  • Deposited Residue Count: 910 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
mAb 3D3 Fab heavy chainA [auth H],
C [auth I]
231Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
mAb 3D3 Fab light chainB [auth L],
D [auth M]
213Homo sapiensMutation(s): 0 
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Major surface glycoprotein GE [auth A],
F [auth B]
11Human respiratory syncytial virus A2Mutation(s): 0 
UniProt
Find proteins for P03423 (Human respiratory syncytial virus A (strain A2))
Explore P03423 
Go to UniProtKB:  P03423
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03423
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
G [auth H]
H
I [auth H]
J [auth H]
K [auth L]
G [auth H],
H,
I [auth H],
J [auth H],
K [auth L],
L,
M [auth L],
O [auth I],
P [auth I],
Q [auth I],
R [auth M],
S [auth M],
U [auth A],
V [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACY

Query on ACY



Download:Ideal Coordinates CCD File
N [auth L],
T [auth M]
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.268 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.76α = 90
b = 105.43β = 90
c = 121.82γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
Cootmodel building
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-03-21
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary