4E68 | pdb_00004e68

Unphosphorylated STAT3B core protein binding to dsDNA

• PDB DOI: https://doi.org/10.2210/pdb4E68/pdb
• NAKB: 4E68

• Classification: TRANSCRIPTION/DNA
• Organism(s): synthetic construct, Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-15 Released: 2013-03-06 
• Deposition Author(s): Collie, G.W., Parkinson, G.N., Shah, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 
  0.273 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Observation of unphosphorylated STAT3 core protein binding to target dsDNA by PEMSA and X-ray crystallography.

Nkansah, E., Shah, R., Collie, G.W., Parkinson, G.N., Palmer, J., Rahman, K.M., Bui, T.T., Drake, A.F., Husby, J., Neidle, S., Zinzalla, G., Thurston, D.E., Wilderspin, A.F.

(2013) FEBS Lett 587: 833-839

• PubMed: 23434585 
• DOI: https://doi.org/10.1016/j.febslet.2013.01.065
• Primary Citation Related Structures: 
  4E68


• PubMed Abstract: 
  

  The STAT3 transcription factor plays a central role in a wide range of cancer types where it is over-expressed. Previously, phosphorylation of this protein was thought to be a prerequisite for direct binding to DNA. However, we have now shown complete binding of a purified unphosphorylated STAT3 (uSTAT3) core directly to M67 DNA, the high affinity STAT3 target DNA sequence, by a protein electrophoretic mobility shift assay (PEMSA). Binding to M67 DNA was inhibited by addition of increasing concentrations of a phosphotyrosyl peptide. X-ray crystallography demonstrates one mode of binding that is similar to that known for the STAT3 core phosphorylated at Y705.

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Organizational Affiliation: 
• Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, London, United Kingdom.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 73.58 kDa 
• Atom Count: 4,998 
• Modeled Residue Count: 577 
• Deposited Residue Count: 614 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal transducer and activator of transcription 3	B [auth A]	596	Mus musculus	Mutation(s): 0  Gene Names: Aprf, Stat3, STAT3B
UniProt
Find proteins for P42227 (Mus musculus) Explore P42227  Go to UniProtKB:  P42227

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*CP*AP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*CP*T)-3')	A [auth B]	18	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free:  0.273 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.14	α = 90
b = 174.14	β = 90
c = 79.29	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
xia2	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-06 
Deposition Author(s): Collie, G.W., Parkinson, G.N., Shah, R.

Revision History  

• Version 1.0: 2013-03-06
  Type: Initial release
  
• Version 1.1: 2013-03-13
  Changes: Database references
• Version 1.2: 2013-04-10
  Changes: Database references
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Refinement description