Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: immunoprecipitation

Macromolecule Content

• Total Structure Weight: 56.08 kDa 
• Atom Count: 2393 
• Residue Count: 241 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

5ZMC

Structural Basis for Reactivation of -146C>T Mutant TERT Promoter by cooperative binding of p52 and ETS1/2

• DOI: 10.2210/pdb5ZMC/pdb
• NDB: 5ZMC

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


• Deposited: 2018-04-02 Released: 2018-09-19 
• Deposition Author(s): Xu, X., Bharath, S.R., Song, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free: 0.288 
• R-Value Work: 0.259 
• R-Value Observed: 0.260 

Literature

Structural basis for reactivating the mutant TERT promoter by cooperative binding of p52 and ETS1.

Xu, X., Li, Y., Bharath, S.R., Ozturk, M.B., Bowler, M.W., Loo, B.Z.L., Tergaonkar, V., Song, H.

(2018) Nat Commun 9: 3183-3183

• PubMed: 30093619 
• DOI: 10.1038/s41467-018-05644-0
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Transcriptional factors ETS1/2 and p52 synergize downstream of non-canonical NF-κB signaling to drive reactivation of the -146C>T mutant TERT promoter in multiple cancer types, but the mechanism underlying this cooperativity remains unknown. Here we report the crystal structure of a ternary p52/ETS1/-146C>T TERT promoter complex. While p52 needs to associate with consensus κB sites on the DNA to function during non-canonical NF-κB signaling, we show that p52 can activate the -146C>T TERT promoter without binding DNA. Instead, p52 interacts with ETS1 to form a heterotetramer, counteracting autoinhibition of ETS1. Analogous to observations with the GABPA/GABPB heterotetramer, the native flanking ETS motifs are required for sustained activation of the -146C>T TERT promoter by the p52/ETS1 heterotetramer. These observations provide a unifying mechanism for transcriptional activation by GABP and ETS1, and suggest that genome-wide targets of non-canonical NF-κB signaling are not limited to those driven by consensus κB sequences.

---

Organizational Affiliation: 

Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore, 117543, Singapore. [e-mail].

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Protein C-ets-1	B	111	Homo sapiens	Mutation(s): 0  Gene Names: ETS1, EWSR2
Find proteins for P14921 (Homo sapiens) Explore P14921  Go to UniProtKB:  P14921
NIH Common Fund Data Resources
PHAROS  P14921 GTEx  ENSG00000134954

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Nuclear factor NF-kappa-B p100 subunit	A	295	Homo sapiens	Mutation(s): 0  Gene Names: NFKB2, LYT10
Find proteins for Q00653 (Homo sapiens) Explore Q00653  Go to UniProtKB:  Q00653
NIH Common Fund Data Resources
PHAROS  Q00653 GTEx  ENSG00000077150

Entity ID: 1
Molecule	Chains	Length	Organism
DNA (5'-D(P*CP*GP*GP*GP*GP*AP*CP*CP*CP*GP*GP*AP*AP*GP*GP*G)-3')	C	16	Homo sapiens

Entity ID: 2
Molecule	Chains	Length	Organism
DNA (5'-D(P*GP*CP*CP*CP*TP*TP*CP*CP*GP*GP*GP*TP*CP*CP*CP*C)-3')	D	16	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free: 0.288 
• R-Value Work: 0.259 
• R-Value Observed: 0.260 
• Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.414	α = 90
b = 71.414	β = 90
c = 262.52	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-04-02 
• Released Date: 2018-09-19 
Deposition Author(s): Xu, X., Bharath, S.R., Song, H.

Revision History 

• Version 1.0: 2018-09-19
  Type: Initial release
  
• Version 1.1: 2018-10-17
  Changes: Data collection, Database references