1NKP

Crystal structure of Myc-Max recognizing DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


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


Literature

X-ray structures of Myc-Max and Mad-Max recognizing DNA: Molecular bases of regulation by proto-oncogenic transcription factors

Nair, S.K., Burley, S.K.

(2003) Cell 112: 193-205

  • DOI: 10.1016/s0092-8674(02)01284-9
  • Primary Citation of Related Structures:  
    1NKP, 1NLW

  • PubMed Abstract: 

    • X-ray structures of the basic/helix-loop-helix/leucine zipper (bHLHZ) domains of Myc-Max and Mad-Max heterodimers bound to their common DNA target (Enhancer or E box hexanucleotide, 5'-CACGTG-3') have been determined at 1.9 A and 2.0 A resolution, respectively ...

    X-ray structures of the basic/helix-loop-helix/leucine zipper (bHLHZ) domains of Myc-Max and Mad-Max heterodimers bound to their common DNA target (Enhancer or E box hexanucleotide, 5'-CACGTG-3') have been determined at 1.9 A and 2.0 A resolution, respectively. E box recognition by these two structurally similar transcription factor pairs determines whether a cell will divide and proliferate (Myc-Max) or differentiate and become quiescent (Mad-Max). Deregulation of Myc has been implicated in the development of many human cancers, including Burkitt's lymphoma, neuroblastomas, and small cell lung cancers. Both quasisymmetric heterodimers resemble the symmetric Max homodimer, albeit with marked structural differences in the coiled-coil leucine zipper regions that explain preferential homo- and heteromeric dimerization of these three evolutionarily related DNA-binding proteins. The Myc-Max heterodimer, but not its Mad-Max counterpart, dimerizes to form a bivalent heterotetramer, which explains how Myc can upregulate expression of genes with promoters bearing widely separated E boxes.

    Organizational Affiliation: 

    Laboratories of Molecular Biophysics, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Myc proto-oncogene proteinE [auth A], G [auth D]88Homo sapiensMutation(s): 0 
Gene Names: MYC, BHLHE39
UniProt & NIH Common Fund Data Resources
Find proteins for P01106 (Homo sapiens)
Explore P01106 
Go to UniProtKB:  P01106
PHAROS:  P01106
GTEx:  ENSG00000136997
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Max proteinF [auth B], H [auth E]83Homo sapiensMutation(s): 0 
Gene Names: MAX, BHLHD4
UniProt & NIH Common Fund Data Resources
Find proteins for P61244 (Homo sapiens)
Explore P61244 
Go to UniProtKB:  P61244
PHAROS:  P61244
GTEx:  ENSG00000125952
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'A [auth F], B [auth G], C [auth H], D [auth J]19N/A
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Binding Affinity Annotations 
    IDSourceBinding Affinity
    DNA PDBBind:  1NKP Kd: 90 (nM) from 1 assay(s)
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.80 Å
    • R-Value Free: 0.263 
    • R-Value Work: 0.219 
    • R-Value Observed: 0.219 
    • Space Group: P 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 39.244α = 87.91
    b = 45.128β = 84.61
    c = 86.484γ = 71.5
    Software Package:
    Software NamePurpose
    HKL-2000data collection
    SCALEPACKdata scaling
    X-PLORmodel building
    CNSrefinement
    HKL-2000data reduction
    X-PLORphasing

    Structure Validation

    View Full Validation Report



    View more in-depth experimental data

    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2003-02-04
      Type: Initial release
    • Version 1.1: 2008-04-29
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2021-02-03
      Changes: Database references, Structure summary