2HDC | pdb_00002hdc

STRUCTURE OF TRANSCRIPTION FACTOR GENESIS/DNA COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb2HDC/pdb
• NAKB: 2HDC

• Classification: PROTEIN/DNA
• Organism(s): Rattus norvegicus
• Mutation(s): No 


• Deposited: 1999-05-05 Released: 1999-07-05 
• Deposition Author(s): Jin, C., Marsden, I., Chen, X., Liao, X.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: LEAST RESTRAINT VIOLATION 

Literature

Dynamic DNA contacts observed in the NMR structure of winged helix protein-DNA complex.

Jin, C., Marsden, I., Chen, X., Liao, X.

(1999) J Mol Biology 289: 683-690

• PubMed: 10369754 
• DOI: https://doi.org/10.1006/jmbi.1999.2819
• Primary Citation Related Structures: 
  2HDC


• PubMed Abstract: 
  

  Genesis is an HNF-3/fkh homologous protein. By using multi-dimensional NMR techniques, we have obtained the solution structure and backbone dynamics of Genesis complexed with a 17 base-pair DNA. Our results indicate that both the local folding and dynamic properties of Genesis are perturbed when it binds to the DNA site. Our data show that a conserved flexible amino acid sequence (wing 1) makes dynamic contacts to DNA in the complex and a short helix is induced by Genesis-DNA interactions. Our data indicate that, unlike the HNF-3gamma/DNA complex, a magnesium ion is not required in forming the stable Genesis-DNA complex.

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Organizational Affiliation: 
• Department or Biochemistry and Molecular Biology, College of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.82 kDa 
• Atom Count: 1,501 
• Modeled Residue Count: 131 
• Deposited Residue Count: 131 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (TRANSCRIPTION FACTOR)	C [auth A]	97	Rattus norvegicus	Mutation(s): 0  Gene Names: GENESIS
UniProt
Find proteins for Q63245 (Rattus norvegicus) Explore Q63245  Go to UniProtKB:  Q63245

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*CP*TP*TP*AP*AP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP*C)-3')	A [auth B]	17	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*TP*TP*AP*AP*GP*C)-3')	B [auth C]	17	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: LEAST RESTRAINT VIOLATION 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-07-05 
Deposition Author(s): Jin, C., Marsden, I., Chen, X., Liao, X.

Revision History  

• Version 1.0: 1999-07-05
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-09
  Changes: Database references, Derived calculations
• Version 1.4: 2023-12-27
  Changes: Data collection