1PUE | pdb_00001pue

PU.1 ETS DOMAIN-DNA COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1PUE/pdb
• NAKB: 1PUE

• Classification: TRANSCRIPTION/DNA
• Organism(s): synthetic construct, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1996-07-08 Released: 1997-02-12 
• Deposition Author(s): Kodandapani, R., Pio, F., Ni, C.Z., Piccialli, G., Klemsz, M., McKercher, S., Maki, R.A., Ely, K.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.287 (Depositor) 
• R-Value Work: 
  0.225 (Depositor) 
• R-Value Observed: 
  0.225 (Depositor) 

Literature

A new pattern for helix-turn-helix recognition revealed by the PU.1 ETS-domain-DNA complex.

Kodandapani, R., Pio, F., Ni, C.Z., Piccialli, G., Klemsz, M., McKercher, S., Maki, R.A., Ely, K.R.

(1996) Nature 380: 456-460

• PubMed: 8602247 
• DOI: https://doi.org/10.1038/380456a0
• Primary Citation Related Structures: 
  1PUE


• PubMed Abstract: 
  

  The Ets family of transcription factors, of which there are now about 35 members regulate gene expression during growth and development. They share a conserved domain of around 85 amino acids which binds as a monomer to the DNA sequence 5'-C/AGGAA/T-3'. We have determined the crystal structure of an ETS domain complexed with DNA, at 2.3-A resolution. The domain is similar to alpha + beta (winged) 'helix-turn-helix' proteins and interacts with a ten-base-pair region of duplex DNA which takes up a uniform curve of 8 degrees. The domain contacts the DNA by a novel loop-helix-loop architecture. Four of amino acids that directly interact with the DNA are highly conserved: two arginines from the recognition helix lying in the major groove, one lysine from the 'wing' that binds upstream of the core GGAA sequence, and another lysine, from the 'turn' of the 'helix-turn-helix' motif, which binds downstream and on the opposite strand.

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Organizational Affiliation: 
• La Jolla Cancer Research Center at the Burnham Institute, California 92037, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 40.81 kDa 
• Atom Count: 2,928 
• Modeled Residue Count: 241 
• Deposited Residue Count: 242 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (TRANSCRIPTION FACTOR PU.1 (TF PU.1))	E, F	89	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P17433 (Mus musculus) Explore P17433  Go to UniProtKB:  P17433
IMPC:  MGI:98282

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*AP*AP*AP*GP*GP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')	A, C	16	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*CP*CP*TP*TP*TP*T)-3')	B, D	16	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.287 (Depositor) 
• R-Value Work:  0.225 (Depositor) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.1	α = 90
b = 101.9	β = 111.2
c = 55.6	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-02-12 
Deposition Author(s): Kodandapani, R., Pio, F., Ni, C.Z., Piccialli, G., Klemsz, M., McKercher, S., Maki, R.A., Ely, K.R.

Revision History  

• Version 1.0: 1997-02-12
  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: 2017-02-15
  Changes: Source and taxonomy, Structure summary
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references