6E29 | pdb_00006e29

Crystal structure of Myceliophteria_thermophila Cps50 (Swd1) beta-propeller domain

• PDB DOI: https://doi.org/10.2210/pdb6E29/pdb

• Classification: PROTEIN BINDING
• Organism(s): Thermothelomyces thermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-07-10 Released: 2018-07-25 
• Deposition Author(s): Joshi, M., Yang, Y., Brunzelle, J.S., Couture, J.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.216 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Structure and Conformational Dynamics of a COMPASS Histone H3K4 Methyltransferase Complex.

Qu, Q., Takahashi, Y.H., Yang, Y., Hu, H., Zhang, Y., Brunzelle, J.S., Couture, J.F., Shilatifard, A., Skiniotis, G.

(2018) Cell 174: 1117

• PubMed: 30100186 
• DOI: https://doi.org/10.1016/j.cell.2018.07.020
• Primary Citation Related Structures: 
  6BX3, 6E29


• PubMed Abstract: 
  

  The methylation of histone 3 lysine 4 (H3K4) is carried out by an evolutionarily conserved family of methyltransferases referred to as complex of proteins associated with Set1 (COMPASS). The activity of the catalytic SET domain (su(var)3-9, enhancer-of-zeste, and trithorax) is endowed through forming a complex with a set of core proteins that are widely shared from yeast to humans. We obtained cryo-electron microscopy (cryo-EM) maps of the yeast Set1/COMPASS core complex at overall 4.0- to 4.4-Å resolution, providing insights into its structural organization and conformational dynamics. The Cps50 C-terminal tail weaves within the complex to provide a central scaffold for assembly. The SET domain, snugly positioned at the junction of the Y-shaped complex, is extensively contacted by Cps60 (Bre2), Cps50 (Swd1), and Cps30 (Swd3). The mobile SET-I motif of the SET domain is engaged by Cps30, explaining its key role in COMPASS catalytic activity toward higher H3K4 methylation states.

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Organizational Affiliation: 
• Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Department of Biochemistry and Molecular Genetics, Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
Department of Biochemistry, Microbiology, and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa ON K1H 8M5, Canada.
Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, IL 60439, USA.
Department of Biochemistry and Molecular Genetics, Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA. Electronic address: [e-mail].
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 156.45 kDa 
• Atom Count: 10,930 
• Modeled Residue Count: 1,268 
• Deposited Residue Count: 1,380 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SWD1-like protein	A [auth D], B [auth A], C [auth B], D [auth C]	345	Thermothelomyces thermophilus	Mutation(s): 0  Gene Names: MYCTH_2294520
UniProt
Find proteins for G2Q1Q9 (Thermothelomyces thermophilus (strain ATCC 42464 / BCRC 31852 / DSM 1799)) Explore G2Q1Q9  Go to UniProtKB:  G2Q1Q9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.216 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.784	α = 90
b = 88.9	β = 94.3
c = 124.319	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-07-25 
Deposition Author(s): Joshi, M., Yang, Y., Brunzelle, J.S., Couture, J.F.

Revision History  

• Version 1.0: 2018-07-25
  Type: Initial release
  
• Version 1.1: 2018-08-29
  Changes: Data collection, Database references
• Version 1.2: 2018-09-05
  Changes: Data collection, Database references
• Version 1.3: 2020-01-22
  Changes: Author supporting evidence
• Version 1.4: 2023-10-11
  Changes: Advisory, Data collection, Database references, Refinement description