6WLA | pdb_00006wla

Antigen binding fragment of ch128.1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.258 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 6WLA

This is version 1.3 of the entry. See complete history

Literature

Host receptor-targeted therapeutic approach to counter pathogenic New World mammarenavirus infections.

Hickerson, B.T.Daniels-Wells, T.R.Payes, C.Clark, L.E.Candelaria, P.V.Bailey, K.W.Sefing, E.J.Zink, S.Ziegenbein, J.Abraham, J.Helguera, G.Penichet, M.L.Gowen, B.B.

(2022) Nat Commun 13: 558-558

  • DOI: https://doi.org/10.1038/s41467-021-27949-3
  • Primary Citation Related Structures: 
    6WLA

  • PubMed Abstract: 

    Five New World mammarenaviruses (NWMs) cause life-threatening hemorrhagic fever (HF). Cellular entry by these viruses is mediated by human transferrin receptor 1 (hTfR1). Here, we demonstrate that an antibody (ch128.1/IgG1) which binds the apical domain of hTfR1, potently inhibits infection of attenuated and pathogenic NWMs in vitro. Computational docking of the antibody Fab crystal structure onto the known structure of hTfR1 shows an overlapping receptor-binding region shared by the Fab and the viral envelope glycoprotein GP1 subunit that binds hTfR1, and we demonstrate competitive inhibition of NWM GP1 binding by ch128.1/IgG1 as the principal mechanism of action. Importantly, ch128.1/IgG1 protects hTfR1-expressing transgenic mice against lethal NWM challenge. Additionally, the antibody is well-tolerated and only partially reduces ferritin uptake. Our findings provide the basis for the development of a novel, host receptor-targeted antibody therapeutic broadly applicable to the treatment of HF of NWM etiology.


  • Organizational Affiliation
    • Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.

Macromolecule Content 

  • Total Structure Weight: 141.14 kDa 
  • Atom Count: 10,024 
  • Modeled Residue Count: 1,290 
  • Deposited Residue Count: 1,290 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab ch128.1 heavy chainA [auth H1],
C [auth H2],
D [auth H3]
219Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab ch128.1 light chainB [auth L1],
E [auth L3],
F [auth L2]
211Homo sapiensMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth H1]
H [auth H1]
I [auth L1]
J [auth L1]
K [auth H2]
G [auth H1],
H [auth H1],
I [auth L1],
J [auth L1],
K [auth H2],
L [auth H2],
M [auth H3],
N [auth L3],
O [auth L2]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.258 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.27α = 90
b = 126.27β = 90
c = 94.85γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States5R21AI135851-02

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2022-02-09
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary