1CF7

STRUCTURAL BASIS OF DNA RECOGNITION BY THE HETERODIMERIC CELL CYCLE TRANSCRIPTION FACTOR E2F-DP

• PDB DOI:  https://doi.org/10.2210/pdb1CF7/pdb
• NAKB: 1CF7

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-03-24 Released: 1999-04-02 
• Deposition Author(s): Zheng, N., Fraenkel, E., Pabo, C.O., Pavletich, N.P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Work: 0.223 

Literature

Structural basis of DNA recognition by the heterodimeric cell cycle transcription factor E2F-DP.

Zheng, N., Fraenkel, E., Pabo, C.O., Pavletich, N.P.

(1999) Genes Dev 13: 666-674

• PubMed: 10090723 
• DOI: https://doi.org/10.1101/gad.13.6.666
• Primary Citation of Related Structures:  
  1CF7


• PubMed Abstract: 
  

The E2F and DP protein families form heterodimeric transcription factors that play a central role in the expression of cell cycle-regulated genes. The crystal structure of an E2F4-DP2-DNA complex shows that the DNA-binding domains of the E2F and DP proteins both have a fold related to the winged-helix DNA-binding motif. Recognition of the central c/gGCGCg/c sequence of the consensus DNA-binding site is symmetric, and amino acids that contact these bases are conserved among all known E2F and DP proteins. The asymmetry in the extended binding site TTTc/gGCGCc/g is associated with an amino-terminal extension of E2F4, in which an arginine binds in the minor groove near the TTT stretch. This arginine is invariant among E2Fs but not present in DPs. E2F4 and DP2 interact through an extensive protein-protein interface, and structural features of this interface suggest it contributes to the preference for heterodimers over homodimers in DNA binding.

---

Organizational Affiliation: 

Howard Hughes Medical Institute, Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021 USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28.98 kDa 
• Atom Count: 1,873 
• Modelled Residue Count: 179 
• Deposited Residue Count: 203 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (TRANSCRIPTION FACTOR E2F-4)	C [auth A]	76	Homo sapiens	Mutation(s): 0  Gene Names: E2F4
UniProt & NIH Common Fund Data Resources
Find proteins for Q16254 (Homo sapiens) Explore Q16254  Go to UniProtKB:  Q16254
PHAROS:  Q16254

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (TRANSCRIPTION FACTOR DP-2)	D [auth B]	95	Homo sapiens	Mutation(s): 0  Gene Names: TFDP2, DP2
UniProt & NIH Common Fund Data Resources
Find proteins for Q14188 (Homo sapiens) Explore Q14188  Go to UniProtKB:  Q14188
PHAROS:  Q14188

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Work: 0.223 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.3	α = 90
b = 101.3	β = 90
c = 73.5	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-04-02 
Deposition Author(s): Zheng, N., Fraenkel, E., Pabo, C.O., Pavletich, N.P.

Revision History  

• Version 1.0: 1999-04-02
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance