2OO4 | pdb_00002oo4

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

• PDB DOI: https://doi.org/10.2210/pdb2OO4/pdb

• Classification: CELL CYCLE,SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-01-25 Released: 2007-04-03 
• Deposition Author(s): Gordon, W.R., Vardar-Ulu, D., Histen, G., Sanchez-Irizarry, C., Aster, J.C., Blacklow, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.268 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

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

• PubMed: 17401372 
• DOI: https://doi.org/10.1038/nsmb1227
• Primary Citation 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 52.97 kDa 
• Atom Count: 3,642 
• Modeled Residue Count: 452 
• Deposited Residue Count: 468 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neurogenic locus notch homolog protein 2	A, B	234	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	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	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	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 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.372	α = 90
b = 74.706	β = 90
c = 139.412	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
SOLOMON	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-03 
Deposition Author(s): Gordon, W.R., Vardar-Ulu, D., Histen, G., Sanchez-Irizarry, C., Aster, J.C., Blacklow, S.C.

Revision History  

• 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