9B3N | pdb_00009b3n

Human Notch-1 EGFs 20-24


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.198 (Depositor), 0.196 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and functional studies of the EGF20-27 region reveal new features of the human Notch receptor important for optimal activation.

Bo, Z.Rowntree, T.Johnson, S.Nurmahdi, H.Suckling, R.J.Hill, J.Korona, B.Weisshuhn, P.C.Sheppard, D.Meng, Y.Liang, S.Lowe, E.D.Lea, S.M.Redfield, C.Handford, P.A.

(2024) Structure 32: 2325-2336.e5

  • DOI: https://doi.org/10.1016/j.str.2024.10.012
  • Primary Citation of Related Structures:  
    9B3G, 9B3N

  • PubMed Abstract: 

    The Notch receptor is activated by the Delta/Serrate/Lag-2 (DSL) family of ligands. The organization of the extracellular signaling complex is unknown, although structures of Notch/ligand complexes comprising the ligand-binding region (LBR), and negative regulatory region (NRR) region, have been solved. Here, we investigate the human Notch-1 epidermal growth factor-like (EGF) 20-27 region, located between the LBR and NRR, and incorporating the Abruptex (Ax) region, associated with distinctive Drosophila phenotypes. Our analyses, using crystallography, NMR and small angle X-ray scattering (SAXS), support a rigid, elongated organization for EGF20-27 with the EGF20-21 linkage showing Ca 2+ -dependent flexibility. In functional assays, Notch-1 variants containing Ax substitutions result in reduced ligand-dependent trans-activation. When cis-JAG1 was expressed, Notch activity differences between WT and Ca 2+ -binding Ax variants were less marked than seen in the trans-activation assays alone, consistent with disruption of cis-inhibition. These data indicate the importance of Ca 2+ -stabilized structure and suggest the balance of cis- and trans-interactions explains the effects of Drosophila Ax mutations.


  • Organizational Affiliation

    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neurogenic locus notch homolog protein 1201Homo sapiensMutation(s): 0 
Gene Names: NOTCH1TAN1
UniProt & NIH Common Fund Data Resources
Find proteins for P46531 (Homo sapiens)
Explore P46531 
Go to UniProtKB:  P46531
PHAROS:  P46531
GTEx:  ENSG00000148400 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46531
Glycosylation
Glycosylation Sites: 6Go to GlyGen: P46531-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-xylopyranose-(1-3)-beta-D-glucopyranose
B
2O-Glycosylation
Glycosylation Resources
GlyTouCan:  G61966PH
GlyCosmos:  G61966PH
GlyGen:  G61966PH
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download Ideal Coordinates CCD File 
C [auth A]beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
FUC
Query on FUC

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A]
alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
K [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.198 (Depositor), 0.196 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.03α = 99.71
b = 35.08β = 92.35
c = 63.89γ = 96.86
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/R009317/1
Medical Research Council (MRC, United Kingdom)United KingdomMR/V008935/1
Wellcome TrustUnited Kingdom100298

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Database references
  • Version 1.2: 2024-12-18
    Changes: Database references