5TDR | pdb_00005tdr

Set3 PHD finger in complex with histone H3K4me2

• PDB DOI: https://doi.org/10.2210/pdb5TDR/pdb

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


• Deposited: 2016-09-19 Released: 2016-11-02 
• Deposition Author(s): Andrews, F.H., Ali, M., Kutateladze, T.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 
  0.200 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Literature

Structural Insight into Recognition of Methylated Histone H3K4 by Set3.

Gatchalian, J., Ali, M., Andrews, F.H., Zhang, Y., Barrett, A.S., Kutateladze, T.G.

(2017) J Mol Biology 429: 2066-2074

• PubMed: 27697561 
• DOI: https://doi.org/10.1016/j.jmb.2016.09.020
• Primary Citation Related Structures: 
  5TDR, 5TDW


• PubMed Abstract: 
  

  The plant homeodomain (PHD) finger of Set3 binds methylated lysine 4 of histone H3 in vitro and in vivo; however, precise selectivity of this domain has not been fully characterized. Here, we explore the determinants of methyllysine recognition by the PHD fingers of Set3 and its orthologs. We use X-ray crystallographic and spectroscopic approaches to show that the Set3 PHD finger binds di- and trimethylated states of H3K4 with comparable affinities and employs similar molecular mechanisms to form complexes with either mark. Composition of the methyllysine-binding pocket plays an essential role in determining the selectivity of the PHD fingers. The finding that the histone-binding activity is not conserved in the PHD finger of Set4 suggests different functions for the Set3 and Set4 paralogs.

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Organizational Affiliation: 
• Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
Structural Biology and Biochemistry Program, University of Colorado School of Medicine, Aurora, CO 80045, USA.
Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Structural Biology and Biochemistry Program, University of Colorado School of Medicine, Aurora, CO 80045, USA. Electronic address: [e-mail].

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: 9.5 kDa 
• Atom Count: 867 
• Modeled Residue Count: 81 
• Deposited Residue Count: 81 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SET domain-containing protein 3	A	70	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SET3, YKR029C
UniProt
Find proteins for P36124 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36124  Go to UniProtKB:  P36124

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	B	11	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	E [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	B	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free:  0.200 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.931	α = 90
b = 43.72	β = 90
c = 84.698	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-02 
Deposition Author(s): Andrews, F.H., Ali, M., Kutateladze, T.G.

Revision History  

• Version 1.0: 2016-11-02
  Type: Initial release
  
• Version 1.1: 2017-06-28
  Changes: Database references
• Version 1.2: 2025-04-02
  Changes: Data collection, Database references, Derived calculations, Structure summary