9FIK | pdb_00009fik

Structure of the FAB fragment of the Antibody NTF30037 in complex with NTF3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 
    0.186 (Depositor), 0.194 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9FIK

This is version 1.1 of the entry. See complete history

Literature

Identification of unique binding mode anti-NTF3 antibodies from a novel long VH CDR3 phage display library.

Chin, S.E.Gallego, P.Aagaard, A.Carmen, S.Barrett, N.Wolny, M.Cloarec, S.Paterson, J.Sivapalan, R.Hunt, J.Murray, T.V.Delaney, T.Sjogren, T.Neal, F.

(2025) SLAS Discov 31: 100216-100216

  • DOI: https://doi.org/10.1016/j.slasd.2025.100216
  • Primary Citation Related Structures: 
    9FIK

  • PubMed Abstract: 

    Neurotrophic factor 3 (NTF3) is a cysteine knot protein and a member of the nerve growth factor (NGF) family of cytokines. NTF3 engages the Trk family of receptor tyrosine kinases, playing a pivotal role in the development and function of both the central and peripheral nervous systems. Its involvement in neuronal survival, differentiation, and growth links NTF3 to a spectrum of neurodegenerative diseases. Consequently, targeting NTF3 with antibodies holds promise as a first in class therapeutic opportunity for a wide range of conditions. Specific and neutralizing antibodies against NTF3 were successfully isolated using phage display. Initial phage display selections revealed a preference of hits for a longer than average complementarity-determining region 3 (CDR3) in the heavy chain variable domain (VH). To investigate this further we developed a long loop length VH CDR3 antibody library that demonstrated increased hit rates versus a standard antibody library and allowed the isolation of IgG that demonstrated inhibition of functional activity, coupled with a favourable kinetic profile. Structural analysis of the Fab/NTF3 interaction, via X-ray crystallography, unveiled an unconventional interaction wherein regions beyond the longer CDR loops of the Fab induced ordering in a flexible loop on NTF3, which remained disordered in its free antigenic state. This comprehensive approach not only sheds light on the therapeutic potential of NTF3-specific antibodies but also provides critical structural details that enhance our understanding of the complex NTF3-Fab interaction thus offering valuable insights for future antibody design and therapeutic development.


  • Organizational Affiliation
    • Biologics Engineering, Oncology R&D, AstraZeneca, Cambridge, UK.

Macromolecule Content 

  • Total Structure Weight: 62.38 kDa 
  • Atom Count: 4,710 
  • Modeled Residue Count: 545 
  • Deposited Residue Count: 571 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Neurotrophin-3120Homo sapiensMutation(s): 0 
Gene Names: NTF3
UniProt & NIH Common Fund Data Resources
Find proteins for P20783 (Homo sapiens)
Explore P20783 
Go to UniProtKB:  P20783
PHAROS:  P20783
GTEx:  ENSG00000185652 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20783
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
NTF30037 Heavy Chain237Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
NTF30037 Light Chain214Homo sapiensMutation(s): 0 

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG

Query on PEG



Download:Ideal Coordinates CCD File
H [auth C],
J [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A],
G [auth B],
I [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
K [auth C]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free:  0.186 (Depositor), 0.194 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.746α = 90
b = 108.549β = 90
c = 208.217γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-02
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Database references