2NNY | pdb_00002nny

Crystal structure of the Ets1 dimer DNA complex.

• PDB DOI: https://doi.org/10.2210/pdb2NNY/pdb
• NAKB: 2NNY

• Classification: Transcription/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-10-24 Released: 2008-03-04 
• Deposition Author(s): Lamber, E.P., Kachalova, G.S., Wilmanns, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 
  0.271 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.235 (DCC) 

Starting Model: experimental

Literature

Regulation of the transcription factor Ets-1 by DNA-mediated homo-dimerization.

Lamber, E.P., Vanhille, L., Textor, L.C., Kachalova, G.S., Sieweke, M.H., Wilmanns, M.

(2008) EMBO J 27: 2006-2017

• PubMed: 18566588 
• DOI: https://doi.org/10.1038/emboj.2008.117
• Primary Citation Related Structures: 
  2NNY


• PubMed Abstract: 
  

  The function of the Ets-1 transcription factor is regulated by two regions that flank its DNA-binding domain. A previously established mechanism for auto-inhibition of monomeric Ets-1 on DNA response elements with a single ETS-binding site, however, has not been observed for the stromelysin-1 promoter containing two palindromic ETS-binding sites. We present the structure of Ets-1 on this promoter element, revealing a ternary complex in which protein homo-dimerization is mediated by the specific arrangement of the two ETS-binding sites. In this complex, the N-terminal-flanking region is required for ternary protein-DNA assembly. Ets-1 variants, in which residues from this region are mutated, loose the ability for DNA-mediated dimerization and stromelysin-1 promoter transactivation. Thus, our data unravel the molecular basis for relief of auto-inhibition and the ability of Ets-1 to function as a facultative dimeric transcription factor on this site. Our findings may also explain previous data of Ets-1 function in the context of heterologous transcription factors, thus providing a molecular model that could also be valid for Ets-1 regulation by hetero-oligomeric assembly.

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Organizational Affiliation: 
• EMBL-Hamburg, c/o DESY, Hamburg, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 53.88 kDa 
• Atom Count: 3,060 
• Modeled Residue Count: 302 
• Deposited Residue Count: 388 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
C-ets-1 protein	C [auth A], D [auth B]	171	Homo sapiens	Mutation(s): 2  Gene Names: ETS1
UniProt & NIH Common Fund Data Resources
Find proteins for P14921 (Homo sapiens) Explore P14921  Go to UniProtKB:  P14921
PHAROS:  P14921 GTEx:  ENSG00000134954

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*T*AP*GP*AP*CP*AP*GP*GP*AP*AP*GP*CP*AP*CP*TP*TP*CP*CP*TP*GP*GP*AP*G)-3'	A [auth C]	23	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*A*CP*TP*CP*CP*AP*GP*GP*AP*AP*GP*TP*GP*CP*TP*TP*CP*CP*TP*GP*TP*CP*T)-3'	B [auth D]	23	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free:  0.271 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.235 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.556	α = 90
b = 100.838	β = 90
c = 69.8	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-04 
Deposition Author(s): Lamber, E.P., Kachalova, G.S., Wilmanns, M.

Revision History  

• Version 1.0: 2008-03-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references
• Version 1.3: 2023-08-30
  Changes: Data collection, Refinement description