3V79 | pdb_00003v79

Structure of human Notch1 transcription complex including CSL, RAM, ANK, and MAML-1 on HES-1 promoter DNA sequence

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.85 Å
  • R-Value Free: 
    0.245 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.213 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history. 

Literature

Conformational Locking upon Cooperative Assembly of Notch Transcription Complexes.

Choi, S.H., Wales, T.E., Nam, Y., O'Donovan, D.J., Sliz, P., Engen, J.R., Blacklow, S.C.

(2012) Structure 20: 340-349

  • DOI: https://doi.org/10.1016/j.str.2011.12.011
  • Primary Citation Related Structures: 
    3V79

  • PubMed Abstract: 

    The Notch intracellular domain (NICD) forms a transcriptional activation complex with the DNA-binding factor CSL and a transcriptional co-activator of the Mastermind family (MAML). The "RAM" region of NICD recruits Notch to CSL, facilitating the binding of MAML at the interface between the ankyrin (ANK) repeat domain of NICD and CSL. Here, we report the X-ray structure of a human MAML1/RAM/ANK/CSL/DNA complex, and probe changes in component dynamics upon stepwise assembly of a MAML1/NICD/CSL complex using HX-MS. Association of CSL with NICD exerts remarkably little effect on the exchange kinetics of the ANK domain, whereas MAML1 binding greatly retards the exchange kinetics of ANK repeats 2-3. These exchange patterns identify critical features contributing to the cooperative assembly of Notch transcription complexes (NTCs), highlight the importance of MAML recruitment in rigidifying the ANK domain and stabilizing its interface with CSL, and rationalize the requirement for MAML1 in driving cooperative dimerization of NTCs on paired-site DNA.

    • Organizational Affiliation: 
    • Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.

Macromolecule Content 

  • Total Structure Weight: 98.13 kDa 
  • Atom Count: 6,421 
  • Modeled Residue Count: 752 
  • Deposited Residue Count: 808 
  • Unique protein chains: 4
  • Unique nucleic acid chains: 2

Macromolecules


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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Neurogenic locus notch homolog protein 1A [auth K]256Homo sapiensMutation(s): 0 
Gene Names: NOTCH1, TAN1
UniProt & NIH Common Fund Data Resources
Find proteins for P46531 (Homo sapiens)
Explore P46531 
Go to UniProtKB:  P46531
PHAROS:  P46531
GTEx:  ENSG00000148400 
Entity Groups
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UniProt GroupP46531
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Reference Sequence
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Recombining binding protein suppressor of hairlessB [auth C]434Homo sapiensMutation(s): 0 
Gene Names: IGKJRB, IGKJRB1, RBPJ, RBPJK, RBPSUH
UniProt & NIH Common Fund Data Resources
Find proteins for Q06330 (Homo sapiens)
Explore Q06330 
Go to UniProtKB:  Q06330
PHAROS:  Q06330
GTEx:  ENSG00000168214 
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UniProt GroupQ06330
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Reference Sequence
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|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Mastermind-like protein 1C [auth M]63Homo sapiensMutation(s): 0 
Gene Names: MAML1, KIAA0200
UniProt & NIH Common Fund Data Resources
Find proteins for Q92585 (Homo sapiens)
Explore Q92585 
Go to UniProtKB:  Q92585
PHAROS:  Q92585
GTEx:  ENSG00000161021 
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UniProt GroupQ92585
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
RAMF [auth R]19Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P46531 (Homo sapiens)
Explore P46531 
Go to UniProtKB:  P46531
PHAROS:  P46531
GTEx:  ENSG00000148400 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46531
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 4
MoleculeChains LengthOrganismImage
DNA 5'-D(*GP*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*AP*AP*A)-3'D [auth X]18N/A
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Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA 5'-D(*TP*TP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*TP*AP*AP*C)-3'E [auth Y]18N/A
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.85 Å
  • R-Value Free:  0.245 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 272.646α = 90
b = 272.646β = 90
c = 119.987γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2012-02-22
    Changes: Database references
  • Version 1.2: 2012-03-21
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Refinement description