1MDY

CRYSTAL STRUCTURE OF MYOD BHLH DOMAIN BOUND TO DNA: PERSPECTIVES ON DNA RECOGNITION AND IMPLICATIONS FOR TRANSCRIPTIONAL ACTIVATION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.253 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of MyoD bHLH domain-DNA complex: perspectives on DNA recognition and implications for transcriptional activation.

Ma, P.C.Rould, M.A.Weintraub, H.Pabo, C.O.

(1994) Cell 77: 451-459

  • DOI: https://doi.org/10.1016/0092-8674(94)90159-7
  • Primary Citation of Related Structures:  
    1MDY

  • PubMed Abstract: 

    The crystal structure of a MyoD basic-helix-loop-helix (bHLH) domain-DNA complex has been solved and refined at 2.8 A resolution. This structure proves that bHLH and bHLH-leucine zipper (bHLH-ZIP) proteins are remarkably similar; it helps us understand subtle differences in binding preferences for these proteins; and it has surprising implications for our understanding of transcription. Specifically, Ala-114 and Thr-115, which are required for positive control in the myogenic proteins, are buried at the protein-DNA interface. These residues are not available for direct protein-protein contacts, but they may determine the conformation of Arg-111. Comparisons with Max suggest that the conformation of this arginine, which is different in the two structures, may play an important role in myogenic transcription.


  • Organizational Affiliation

    Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge 02139.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (MYOD BHLH DOMAIN)E [auth A]68Mus musculusMutation(s): 0 
UniProt
Find proteins for P10085 (Mus musculus)
Explore P10085 
Go to UniProtKB:  P10085
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10085
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (MYOD BHLH DOMAIN)F [auth B],
G [auth C],
H [auth D]
62Mus musculusMutation(s): 0 
UniProt
Find proteins for P10085 (Mus musculus)
Explore P10085 
Go to UniProtKB:  P10085
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10085
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*CP*AP*AP*CP*AP*GP*CP*TP*GP*TP*TP*GP*A)-3')A [auth E],
B [auth F],
C [auth G],
D [auth H]
14N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.253 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 222.8α = 90
b = 70.8β = 90
c = 30γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
TNTrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-08-31
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references