4N0A | pdb_00004n0a

Crystal structure of Lsm2-3-Pat1C complex from Saccharomyces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb4N0A/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-10-01 Released: 2013-12-04 
• Deposition Author(s): Wu, D.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.300 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.272 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.274 (Depositor) 

Literature

Lsm2 and Lsm3 bridge the interaction of the Lsm1-7 complex with Pat1 for decapping activation

Wu, D., Muhlrad, D., Bowler, M.W., Jiang, S., Liu, Z., Parker, R., Song, H.

(2014) Cell Res 24: 233-246

• PubMed: 24247251 
• DOI: https://doi.org/10.1038/cr.2013.152
• Primary Citation Related Structures: 
  4N0A


• PubMed Abstract: 
  

  The evolutionarily conserved Lsm1-7-Pat1 complex is the most critical activator of mRNA decapping in eukaryotic cells and plays many roles in normal decay, AU-rich element-mediated decay, and miRNA silencing, yet how Pat1 interacts with the Lsm1-7 complex is unknown. Here, we show that Lsm2 and Lsm3 bridge the interaction between the C-terminus of Pat1 (Pat1C) and the Lsm1-7 complex. The Lsm2-3-Pat1C complex and the Lsm1-7-Pat1C complex stimulate decapping in vitro to a similar extent and exhibit similar RNA-binding preference. The crystal structure of the Lsm2-3-Pat1C complex shows that Pat1C binds to Lsm2-3 to form an asymmetric complex with three Pat1C molecules surrounding a heptameric ring formed by Lsm2-3. Structure-based mutagenesis revealed the importance of Lsm2-3-Pat1C interactions in decapping activation in vivo. Based on the structure of Lsm2-3-Pat1C, a model of Lsm1-7-Pat1 complex is constructed and how RNA binds to this complex is discussed.

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Organizational Affiliation: 
• Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673.
Department of Biochemistry and Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder CO 80303, USA.
1] European Molecular Biology Laboratory, 6 rue Jules Horowitz, BP 181, 38042, Grenoble, France [2] Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France.
Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou, Zhejiang 310000, China.
1] Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673 [2] Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou, Zhejiang 310000, China [3] Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore 117543.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 14-mer - A8B6 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 14-mer - A14 

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

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: 208.12 kDa 
• Atom Count: 12,345 
• Modeled Residue Count: 1,512 
• Deposited Residue Count: 1,823 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
U6 snRNA-associated Sm-like protein LSm3	A, B, E, F	89	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: LSM3, SMX4, USS2, YLR438C-A
UniProt
Find proteins for P57743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P57743  Go to UniProtKB:  P57743

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
U6 snRNA-associated Sm-like protein LSm2	C, D, G	109	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: LSM2, SMX5, SNP3, YBL026W, YBL0425
UniProt
Find proteins for P38203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38203  Go to UniProtKB:  P38203

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 2-associated protein PAT1	H, I, J	380	Saccharomyces cerevisiae S288C	Mutation(s): 1  Gene Names: MRT1, PAT1, YCR077C, YCR77C
UniProt
Find proteins for P25644 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25644  Go to UniProtKB:  P25644

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.300 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.272 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.274 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.447	α = 90
b = 251.511	β = 112.09
c = 120.31	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
PHENIX	model building
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-04 
Deposition Author(s): Wu, D.H.

Revision History  

• Version 1.0: 2013-12-04
  Type: Initial release
  
• Version 1.1: 2014-01-22
  Changes: Database references
• Version 1.2: 2014-02-19
  Changes: Database references
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references