2OO4

Structure of LNR-HD (Negative Regulatory Region) from human Notch 2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history. 


Literature

Structural basis for autoinhibition of Notch

Gordon, W.R., Vardar-Ulu, D., Histen, G., Sanchez-Irizarry, C., Aster, J.C., Blacklow, S.C.

(2007) Nat Struct Mol Biol 14: 295-300

  • DOI: https://doi.org/10.1038/nsmb1227
  • Primary Citation of Related Structures:  
    2OO4

  • PubMed Abstract: 

    Notch receptors transmit signals between adjacent cells. Signaling is initiated when ligand binding induces metalloprotease cleavage of Notch within an extracellular negative regulatory region (NRR). We present here the X-ray structure of the human NOTCH2 NRR, which adopts an autoinhibited conformation. Extensive interdomain interactions within the NRR bury the metalloprotease site, showing that a substantial conformational movement is necessary to expose this site during activation by ligand. Leukemia-associated mutations in NOTCH1 probably release autoinhibition by destabilizing the conserved hydrophobic core of the NRR.

    • Organizational Affiliation: 

    Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, 77 Ave. Louis Pasteur, Boston, Massachusetts 02115, USA.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neurogenic locus notch homolog protein 2
A, B
234Homo sapiensMutation(s): 0 
Gene Names: NOTCH2
UniProt & NIH Common Fund Data Resources
Find proteins for Q04721 (Homo sapiens)
Explore Q04721 
Go to UniProtKB:  Q04721
PHAROS:  Q04721
GTEx:  ENSG00000134250 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04721
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
R [auth B],
S [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
F [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
O [auth B]
P [auth B]
C [auth A],
D [auth A],
E [auth A],
O [auth B],
P [auth B],
Q [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.372α = 90
b = 74.706β = 90
c = 139.412γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLOMONphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-03
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2015-04-08
    Changes: Database references
  • Version 1.4: 2017-10-18
    Changes: Refinement description
  • Version 1.5: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.6: 2024-11-20
    Changes: Structure summary