3U1M | pdb_00003u1m

Structure of the mRNA splicing complex component Cwc2

• PDB DOI: https://doi.org/10.2210/pdb3U1M/pdb

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


• Deposited: 2011-09-30 Released: 2011-11-16 
• Deposition Author(s): Lu, P., Lu, G., Yan, C., Wang, L., Li, W., Yin, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.191 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Structure of the mRNA splicing complex component Cwc2: insights into RNA recognition

Lu, P., Lu, G., Yan, C., Wang, L., Li, W., Yin, P.

(2012) Biochem J 441: 591-597

• PubMed: 21957909 
• DOI: https://doi.org/10.1042/BJ20111385
• Primary Citation Related Structures: 
  3U1L, 3U1M


• PubMed Abstract: 
  

  The Prp19-associated complex [NTC (nineteen complex)] plays a crucial role in intron removal during premature mRNA splicing in eukaryotes. Only one component of the NTC, Cwc2, is capable of binding RNA. In the present study we report the 1.9 Å (1 Å=0.1 nm) X-ray structure of the Cwc2 core domain, which is both necessary and sufficient for RNA binding. The Cwc2 core domain contains two sub-domains, a CCCH-type ZnF (zinc finger) and a RRM (RNA recognition motif). Unexpectedly, the ZnF domain and the RRM form a single folding unit, glued together by extensive hydrophobic interactions and hydrogen bonds. Structure-guided mutational analysis revealed that the intervening loop [known as the RB loop (RNA-binding loop)] between ZnF and RRM plays an essential role in RNA binding. In addition, a number of highly conserved positively charged residues on the β-strands of RRM make an important contribution to RNA binding. Intriguingly, these residues and a portion of the RB loop constitute an extended basic surface strip that encircles Cwc2 halfway. The present study serves as a framework for understanding the regulatory function of the NTC in RNA splicing.

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Organizational Affiliation: 
• Center of Structural Biology, Tsinghua University, Beijing 100084, China.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 27.44 kDa 
• Atom Count: 2,111 
• Modeled Residue Count: 221 
• Deposited Residue Count: 240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pre-mRNA-splicing factor CWC2	A	240	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: CWC2, NTC40, SLC3, YDL209C, D1041
UniProt
Find proteins for Q12046 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12046  Go to UniProtKB:  Q12046

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.191 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.719	α = 90
b = 54.34	β = 90
c = 111.381	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-16 
Deposition Author(s): Lu, P., Lu, G., Yan, C., Wang, L., Li, W., Yin, P.

Revision History  

• Version 1.0: 2011-11-16
  Type: Initial release
  
• Version 1.1: 2014-02-05
  Changes: Database references
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description