6XSW

Structure of the Notch3 NRR in complex with an antibody Fab Fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

NOTCH3-targeted antibody drug conjugates regress tumors by inducing apoptosis in receptor cells and through transendocytosis into ligand cells.

Geles, K.G.Gao, Y.Giannakou, A.Sridharan, L.Yamin, T.T.Zhang, J.Karim, R.Bard, J.Piche-Nicholas, N.Charati, M.Maderna, A.Lucas, J.Golas, J.Guffroy, M.Pirie-Shepherd, S.Roy, M.Qian, J.Franks, T.Zhong, W.O'Donnell, C.J.Tchistiakova, L.Gerber, H.P.Sapra, P.

(2021) Cell Rep Med 2: 100279-100279

  • DOI: https://doi.org/10.1016/j.xcrm.2021.100279
  • Primary Citation of Related Structures:  
    6XSW

  • PubMed Abstract: 

    Aberrant NOTCH3 signaling and overexpression is oncogenic, associated with cancer stem cells and drug resistance, yet therapeutic targeting remains elusive. Here, we develop NOTCH3-targeted antibody drug conjugates (NOTCH3-ADCs) by bioconjugation of an auristatin microtubule inhibitor through a protease cleavable linker to two antibodies with differential abilities to inhibit signaling. The signaling inhibitory antibody rapidly induces ligand-independent receptor clustering and internalization through both caveolin and clathrin-mediated pathways. The non-inhibitory antibody also efficiently endocytoses via clathrin without inducing receptor clustering but with slower lysosomal co-localization kinetics. In addition, DLL4 ligand binding to the NOTCH3 receptor mediates transendocytosis of NOTCH3-ADCs into ligand-expressing cells. NOTCH3-ADCs internalize into receptor and ligand cells independent of signaling and induce cell death in both cell types representing an atypical mechanism of ADC cytotoxicity. Treatment of xenografts with NOTCH3-ADCs leads to sustained tumor regressions, outperforms standard-of-care chemotherapy, and allows targeting of tumors that overexpress NOTCH3 independent of signaling inhibition.


  • Organizational Affiliation

    Pfizer Worldwide Research and Development, Oncology Research and Development, Pearl River, NY, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Anti-N3 Fab Heavy Chain
A, D, G, H
231Rattus norvegicusMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Anti-N3 Fab Light ChainB,
E,
I,
K [auth L]
214Rattus norvegicusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Neurogenic locus notch homolog protein 3C,
F,
J,
L [auth X]
280Homo sapiensMutation(s): 0 
Gene Names: NOTCH3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UM47 (Homo sapiens)
Explore Q9UM47 
Go to UniProtKB:  Q9UM47
PHAROS:  Q9UM47
GTEx:  ENSG00000074181 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UM47
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q9UM47-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseM [auth P]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
Q [auth C],
U [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth X]
BA [auth X]
N [auth C]
O [auth C]
P [auth C]
AA [auth X],
BA [auth X],
N [auth C],
O [auth C],
P [auth C],
R [auth F],
S [auth F],
T [auth F],
V [auth J],
W [auth J],
X [auth J],
Y [auth X],
Z [auth X]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.652α = 90
b = 158.951β = 90
c = 159.687γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2021-07-21 
  • Deposition Author(s): Bard, J.

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-21
    Type: Initial release
  • Version 1.1: 2023-02-01
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description