5FMA | pdb_00005fma

human Notch 1, EGF 4-7

• PDB DOI: https://doi.org/10.2210/pdb5FMA/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-11-02 Released: 2016-04-13 
• Deposition Author(s): Weisshuhn, P.C., Sheppard, D., Taylor, P., Whiteman, P., Lea, S.M., Handford, P.A., Redfield, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.263 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.259 (Depositor), 0.274 (DCC) 
• R-Value Observed: 
  0.259 (Depositor) 

Starting Model: experimental

Literature

Non-Linear and Flexible Regions of the Human Notch1 Extracellular Domain Revealed by High-Resolution Structural Studies.

Weisshuhn, P.C., Sheppard, D., Taylor, P., Whiteman, P., Lea, S.M., Handford, P.A., Redfield, C.

(2016) Structure 24: 555

• PubMed: 26996961 
• DOI: https://doi.org/10.1016/j.str.2016.02.010
• Primary Citation Related Structures: 
  5FM9, 5FMA


• PubMed Abstract: 
  

  The Notch receptor is a key component of a core metazoan signaling pathway activated by Delta/Serrate/Lag-2 ligands expressed on an adjacent cell. This results in a short-range signal with profound effects on cell-fate determination, cell proliferation, and cell death. Key to understanding receptor function is structural knowledge of the large extracellular portion of Notch which contains multiple repeats of epidermal growth factor (EGF)-like domains. Here we investigate the EGF4-13 region of human Notch1 (hN1) using a multidisciplinary approach. Ca(2+)-binding measurements, X-ray crystallography, {(1)H}-(15)N heteronuclear nuclear Overhauser effects, and residual dipolar couplings support a non-linear organization for the EGF4-13 region with a rigid, bent conformation for EGF4-7 and a single flexible linkage between EGF9 and EGF10. These data allow us to construct an informed model for EGF10-13 which, in conjunction with comparative binding studies, demonstrates that EGF10 has an important role in determining Notch receptor sensitivity to Dll-4.

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Organizational Affiliation: 
• Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK. Electronic address: [e-mail].
Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.16 kDa 
• Atom Count: 2,254 
• Modeled Residue Count: 303 
• Deposited Residue Count: 308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1	A, B	154	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P46531 (Homo sapiens) Explore P46531  Go to UniProtKB:  P46531
PHAROS:  P46531 GTEx:  ENSG00000148400

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	H [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free:  0.263 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.259 (Depositor), 0.274 (DCC) 
• R-Value Observed: 0.259 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.94	α = 90
b = 86.83	β = 107.58
c = 53.45	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-13 
Deposition Author(s): Weisshuhn, P.C., Sheppard, D., Taylor, P., Whiteman, P., Lea, S.M., Handford, P.A., Redfield, C.

Revision History  

• Version 1.0: 2016-04-13
  Type: Initial release
  
• Version 1.1: 2016-04-20
  Changes: Database references
• Version 1.2: 2018-02-07
  Changes: Structure summary
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary