6DEI

Structure of Dse3-Csm1 complex

• PDB DOI: https://doi.org/10.2210/pdb6DEI/pdb

• Classification: Protein Binding/Cell Cycle
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-05-12 Released: 2018-10-03 
• Deposition Author(s): Singh, N., Corbett, K.D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.221 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Starting Model: experimental

Literature

The budding-yeast RWD protein Csm1 scaffolds diverse protein complexes through a conserved structural mechanism.

Singh, N., Corbett, K.D.

(2018) Protein Sci 27: 2094-2100

• PubMed: 30252178 
• DOI: https://doi.org/10.1002/pro.3515
• Primary Citation of Related Structures:  
  6DEI


• PubMed Abstract: 
  

  RWD domains mediate protein-protein interactions in a variety of pathways in eukaryotes. In budding yeast, the RWD domain protein Csm1 is particularly versatile, assembling key complexes in the nucleolus and at meiotic kinetochores through multiple protein interaction surfaces. Here, we reveal a third functional context for Csm1 by identifying a new Csm1-interacting protein, Dse3. We show that Dse3 interacts with Csm1 in a structurally equivalent manner to its known binding partners Mam1 and Ulp2, despite these three proteins' lack of overall sequence homology. We theorize that the unique "clamp" structure of Csm1 and the loose sequence requirements for Csm1 binding have led to its incorporation into at least three different structural/signaling pathways in budding yeast.

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Organizational Affiliation: 

Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, California, 92093.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 31.75 kDa 
• Atom Count: 2,318 
• Modelled Residue Count: 253 
• Deposited Residue Count: 274 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Monopolin complex subunit CSM1	A, B	113	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: CSM1, SPO86, YCR086W, YCR86W
UniProt
Find proteins for P25651 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25651  Go to UniProtKB:  P25651

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein DSE3	C, D	24	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: DSE3, YOR264W
UniProt
Find proteins for Q08729 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08729  Go to UniProtKB:  Q08729

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	E [auth A], G [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
ACT	F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.221 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.15785/SBGRID/585

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.442	α = 90
b = 51.235	β = 90
c = 117.848	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-03 
Deposition Author(s): Singh, N., Corbett, K.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM104141

Revision History  

• Version 1.0: 2018-10-03
  Type: Initial release
  
• Version 1.1: 2018-10-10
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2018-11-14
  Changes: Data collection, Database references, Structure summary
• Version 1.3: 2018-11-28
  Changes: Data collection, Database references
• Version 1.4: 2020-01-01
  Changes: Author supporting evidence
• Version 1.5: 2023-10-11
  Changes: Data collection, Database references, Refinement description