4XL1

Complex of Notch1 (EGF11-13) bound to Delta-like 4 (N-EGF1)

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

  • Deposited: 2015-01-13 Released: 2015-03-04 
  • Deposition Author(s): Luca, V.C., Jude, K.M., Garcia, K.C.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI), Ludwig Cancer Foundation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Structural biology. Structural basis for Notch1 engagement of Delta-like 4.

Luca, V.C.Jude, K.M.Pierce, N.W.Nachury, M.V.Fischer, S.Garcia, K.C.

(2015) Science 347: 847-853

  • DOI: 10.1126/science.1261093
  • Primary Citation of Related Structures:  
    4XL1, 4XLW

  • PubMed Abstract: 
  • Notch receptors guide mammalian cell fate decisions by engaging the proteins Jagged and Delta-like (DLL). The 2.3 angstrom resolution crystal structure of the interacting regions of the Notch1-DLL4 complex reveals a two-site, antiparallel binding orientation assisted by Notch1 O-linked glycosylation ...

    Notch receptors guide mammalian cell fate decisions by engaging the proteins Jagged and Delta-like (DLL). The 2.3 angstrom resolution crystal structure of the interacting regions of the Notch1-DLL4 complex reveals a two-site, antiparallel binding orientation assisted by Notch1 O-linked glycosylation. Notch1 epidermal growth factor-like repeats 11 and 12 interact with the DLL4 Delta/Serrate/Lag-2 (DSL) domain and module at the N-terminus of Notch ligands (MNNL) domains, respectively. Threonine and serine residues on Notch1 are functionalized with O-fucose and O-glucose, which act as surrogate amino acids by making specific, and essential, contacts to residues on DLL4. The elucidation of a direct chemical role for O-glycans in Notch1 ligand engagement demonstrates how, by relying on posttranslational modifications of their ligand binding sites, Notch proteins have linked their functional capacity to developmentally regulated biosynthetic pathways.


    Organizational Affiliation

    Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. kcgarcia@stanford.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Neurogenic locus notch homolog protein 1A,
C [auth D]
118Rattus norvegicusMutation(s): 0 
Gene Names: Notch1
UniProt
Find proteins for Q07008 (Rattus norvegicus)
Explore Q07008 
Go to UniProtKB:  Q07008
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07008
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Delta-like proteinB,
D [auth E]
230Rattus norvegicusMutation(s): 3 
Gene Names: Dll4Dll4_predictedrCG_26804
UniProt
Find proteins for D3ZHH1 (Rattus norvegicus)
Explore D3ZHH1 
Go to UniProtKB:  D3ZHH1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD3ZHH1
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth C],
F
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
N [auth B],
O [auth B],
W [auth E],
X [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BGC
Query on BGC

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
J [auth A],
P [auth D],
Q [auth D],
G [auth A],
H [auth A],
J [auth A],
P [auth D],
Q [auth D],
S [auth D]
beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
FUC
Query on FUC

Download Ideal Coordinates CCD File 
I [auth A],
R [auth D]
alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A],
M [auth A],
T [auth D],
U [auth D],
K [auth A],
L [auth A],
M [auth A],
T [auth D],
U [auth D],
V [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
B,
D [auth E]
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.809α = 90
b = 93.7β = 90
c = 99.126γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM097015
Howard Hughes Medical Institute (HHMI)United States--
Ludwig Cancer FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-03-11
    Changes: Database references
  • Version 1.2: 2015-07-15
    Changes: Derived calculations
  • Version 1.3: 2017-09-20
    Changes: Advisory, Author supporting evidence, Derived calculations, Source and taxonomy
  • Version 1.4: 2019-11-20
    Changes: Author supporting evidence, Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary