5IOK

Crystal structure of Taf14 YEATS domain in complex with histone H3K9cr

• PDB DOI: https://doi.org/10.2210/pdb5IOK/pdb

• Classification: TRANSCRIPTION
• Organism(s): Saccharomyces cerevisiae S288C, Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-03-08 Released: 2016-04-20 
• Deposition Author(s): Andrews, F.H., Kuateladze, T.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.239 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 

Starting Model: experimental

Literature

The Taf14 YEATS domain is a reader of histone crotonylation.

Andrews, F.H., Shinsky, S.A., Shanle, E.K., Bridgers, J.B., Gest, A., Tsun, I.K., Krajewski, K., Shi, X., Strahl, B.D., Kutateladze, T.G.

(2016) Nat Chem Biol 12: 396-398

• PubMed: 27089029 
• DOI: https://doi.org/10.1038/nchembio.2065
• Primary Citation of Related Structures:  
  5IOK


• PubMed Abstract: 
  

  The discovery of new histone modifications is unfolding at startling rates; however, the identification of effectors capable of interpreting these modifications has lagged behind. Here we report the YEATS domain as an effective reader of histone lysine crotonylation, an epigenetic signature associated with active transcription. We show that the Taf14 YEATS domain engages crotonyllysine via a unique π-π-π-stacking mechanism and that other YEATS domains have crotonyllysine-binding activity.

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Organizational Affiliation: 

Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 17.28 kDa 
• Atom Count: 1,365 
• Modelled Residue Count: 150 
• Deposited Residue Count: 150 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor TFIID subunit 14	A	142	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: TAF14, ANC1, CST10, SWP29, TAF30, TFG3, YPL129W
UniProt
Find proteins for P35189 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P35189  Go to UniProtKB:  P35189

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
(ACE)QTAR(KCR)ST	B [auth C]	8	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P61830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P61830  Go to UniProtKB:  P61830

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	C [auth A], D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCR	B [auth C]	L-PEPTIDE LINKING	C10 H18 N2 O3		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.239 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.095	α = 90
b = 113.095	β = 90
c = 26.176	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-20 
Deposition Author(s): Andrews, F.H., Kuateladze, T.G.

Revision History  

• Version 1.0: 2016-04-20
  Type: Initial release
  
• Version 1.1: 2016-05-04
  Changes: Database references
• Version 1.2: 2016-06-01
  Changes: Database references
• Version 1.3: 2017-08-23
  Changes: Data collection, Derived calculations
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2023-11-15
  Changes: Data collection