4B0A | pdb_00004b0a

The high-resolution structure of yTBP-yTAF1 identifies conserved and competing interaction surfaces in transcriptional activation

• PDB DOI: https://doi.org/10.2210/pdb4B0A/pdb

• Classification: TRANSCRIPTION
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2012-06-29 Released: 2013-07-03 
• Deposition Author(s): Anandapadamanaban, M., Andresen, C., Siponen, M., Kokubo, T., Ikura, M., Moche, M., Sunnerhagen, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.223 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.164 (Depositor) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

High-Resolution Structure of TBP with Taf1 Reveals Anchoring Patterns in Transcriptional Regulation

Anandapadamanaban, M., Andresen, C., Siponen, M., Kokubo, T., Ikura, M., Moche, M., Sunnerhagen, M.

(2013) Nat Struct Mol Biol 20: 1008

• PubMed: 23851461 
• DOI: https://doi.org/10.1038/nsmb.2611
• Primary Citation Related Structures: 
  4B0A


• PubMed Abstract: 
  

  The general transcription factor TFIID provides a regulatory platform for transcription initiation. Here we present the crystal structure (1.97 Å) and NMR analysis of yeast TAF1 N-terminal domains TAND1 and TAND2 bound to yeast TBP, together with mutational data. We find that yeast TAF1-TAND1, which in itself acts as a transcriptional activator, binds TBP's concave DNA-binding surface by presenting similar anchor residues to TBP as does Mot1 but from a distinct structural scaffold. Furthermore, we show how TAF1-TAND2 uses an aromatic and acidic anchoring pattern to bind a conserved TBP surface groove traversing the basic helix region, and we find highly similar TBP-binding motifs also presented by the structurally distinct TFIIA, Mot1 and Brf1 proteins. Our identification of these anchoring patterns, which can be easily disrupted or enhanced, provides insight into the competitive multiprotein TBP interplay critical to transcriptional regulation.

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Organizational Affiliation: 
• Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 31.02 kDa 
• Atom Count: 2,189 
• Modeled Residue Count: 237 
• Deposited Residue Count: 278 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 1, LINKER, TATA-BOX-BINDING PROTEIN	A	278	Saccharomyces cerevisiae	Mutation(s): 2  EC: 2.3.1.48
UniProt
Find proteins for P13393 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P13393  Go to UniProtKB:  P13393
Find proteins for P46677 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P46677  Go to UniProtKB:  P46677
UniProt Groups	P13393P46677

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	B [auth A], C [auth A], J [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.223 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.164 (Depositor) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.894	α = 90
b = 74.253	β = 90
c = 99.667	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-03 
Deposition Author(s): Anandapadamanaban, M., Andresen, C., Siponen, M., Kokubo, T., Ikura, M., Moche, M., Sunnerhagen, M.

Revision History  

• Version 1.0: 2013-07-03
  Type: Initial release
  
• Version 1.1: 2013-07-17
  Changes: Database references
• Version 1.2: 2013-07-24
  Changes: Database references
• Version 1.3: 2013-08-21
  Changes: Database references
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description