1MSF

SOLUTION STRUCTURE OF A SPECIFIC DNA COMPLEX OF THE MYB DNA-BINDING DOMAIN WITH COOPERATIVE RECOGNITION HELICES

• PDB DOI: https://doi.org/10.2210/pdb1MSF/pdb
• NAKB: 1MSF

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1995-01-24 Released: 1995-03-31 
• Deposition Author(s): Ogata, K., Morikawa, S., Nakamura, H., Sekikawa, A., Inoue, T., Kanai, H., Sarai, A., Ishii, S., Nishimura, Y.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 25 

Literature

Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices.

Ogata, K., Morikawa, S., Nakamura, H., Sekikawa, A., Inoue, T., Kanai, H., Sarai, A., Ishii, S., Nishimura, Y.

(1994) Cell 79: 639-648

• PubMed: 7954830 
• DOI: https://doi.org/10.1016/0092-8674(94)90549-5
• Primary Citation of Related Structures:  
  1MSE, 1MSF


• PubMed Abstract: 
  

  The DNA-binding region of Myb consists of three imperfect tandem repeats (R1, R2, and R3). We have determined the solution structure of a specific DNA complex of the minimum DNA-binding domain (R2R3) by heteronuclear multidimensional NMR. Both R2 and R3 contain three helices, and the third helix in each is found to be a recognition helix. R2 and R3 are closely packed in the major groove, so that the two recognition helices contact each other directly to bind to the specific base sequence, AACNG cooperatively; this is a significant arrangement of recognition helices. The three key base pairs in this sequence are specifically recognized by Asn-183 (R3), Lys-182 (R3), and Lys-128 (R2). In contrast, R1 has no specific interactions with DNA from our NMR study of the DNA complex of the full DNA-binding domain (R1R2R3).

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Organizational Affiliation: 

Graduate School of Integrated Science, Yokohama City University, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 22.47 kDa 
• Atom Count: 1,341 
• Modelled Residue Count: 127 
• Deposited Residue Count: 137 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
C-Myb DNA-Binding Domain	C	105	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P06876 (Mus musculus) Explore P06876  Go to UniProtKB:  P06876
IMPC:  MGI:97249

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*TP*AP*AP*CP*TP*GP*AP*CP*AP*CP*AP*CP*AP*T)-3')	A	16	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*GP*TP*GP*TP*GP*TP*CP*AP*GP*TP*TP*AP*GP*G)-3')	B	16	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 25 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-03-31 
Deposition Author(s): Ogata, K., Morikawa, S., Nakamura, H., Sekikawa, A., Inoue, T., Kanai, H., Sarai, A., Ishii, S., Nishimura, Y.

Revision History  

• Version 1.0: 1995-03-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Database references, Derived calculations, Other
• Version 1.4: 2024-05-22
  Changes: Data collection