5UK5

Complex of Notch1(EGF8-12) bound to Jagged1(N-EGF3)

  • Classification: SIGNALING PROTEIN
  • Organism(s): Rattus norvegicus
  • Expression System: Trichoplusia ni
  • Mutation(s): 

  • Deposited: 2017-01-19 Released: 2017-03-08 
  • Deposition Author(s): Garcia, K.C., Luca, V.C.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences; Howard Hughes Medical Institute; Ludwig Cancer Foundation 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.506 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Notch-Jagged complex structure implicates a catch bond in tuning ligand sensitivity.

Luca, V.C.Kim, B.C.Ge, C.Kakuda, S.Wu, D.Roein-Peikar, M.Haltiwanger, R.S.Zhu, C.Ha, T.Garcia, K.C.

(2017) Science 355: 1320-1324

  • DOI: 10.1126/science.aaf9739

  • PubMed Abstract: 
  • Notch receptor activation initiates cell fate decisions and is distinctive in its reliance on mechanical force and protein glycosylation. The 2.5-angstrom-resolution crystal structure of the extracellular interacting region of Notch1 complexed with a ...

    Notch receptor activation initiates cell fate decisions and is distinctive in its reliance on mechanical force and protein glycosylation. The 2.5-angstrom-resolution crystal structure of the extracellular interacting region of Notch1 complexed with an engineered, high-affinity variant of Jagged1 (Jag1) reveals a binding interface that extends ~120 angstroms along five consecutive domains of each protein. O-Linked fucose modifications on Notch1 epidermal growth factor-like (EGF) domains 8 and 12 engage the EGF3 and C2 domains of Jag1, respectively, and different Notch1 domains are favored in binding to Jag1 than those that bind to the Delta-like 4 ligand. Jag1 undergoes conformational changes upon Notch binding, exhibiting catch bond behavior that prolongs interactions in the range of forces required for Notch activation. This mechanism enables cellular forces to regulate binding, discriminate among Notch ligands, and potentiate Notch signaling.


    Organizational Affiliation

    Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neurogenic locus notch homolog protein 1
A
205Rattus norvegicusMutation(s): 0 
Gene Names: Notch1
Find proteins for Q07008 (Rattus norvegicus)
Go to UniProtKB:  Q07008
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein jagged-1
B
318Rattus norvegicusMutation(s): 5 
Gene Names: Jag1
Find proteins for Q63722 (Rattus norvegicus)
Go to UniProtKB:  Q63722
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BGC
Query on BGC

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Download CCD File 
A
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
XYS
Query on XYS

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Download CCD File 
A
XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-LECHCGJUSA-N
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
A, B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
B
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.506 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.219 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.457α = 90.00
b = 127.995β = 90.00
c = 154.288γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
DENZOdata reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesNIH-1R01-GM097015
Howard Hughes Medical InstituteUnited States--
Ludwig Cancer FoundationUnited States--

Revision History 

  • Version 1.0: 2017-03-08
    Type: Initial release
  • Version 1.1: 2017-03-15
    Type: Database references
  • Version 1.2: 2017-04-12
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Refinement description
  • Version 1.4: 2018-01-24
    Type: Structure summary