4DGW

Crystal Structure of the SF3a splicing factor complex of U2 snRNP

• PDB DOI: https://doi.org/10.2210/pdb4DGW/pdb

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


• Deposited: 2012-01-26 Released: 2012-05-02 
• Deposition Author(s): Lin, P.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.11 Å
• R-Value Free: 0.278 
• R-Value Work: 0.228 
• R-Value Observed: 0.233 

Literature

Structure and assembly of the SF3a splicing factor complex of U2 snRNP

Lin, P.C., Xu, R.M.

(2012) EMBO J 31: 1579-1590

• PubMed: 22314233 
• DOI: https://doi.org/10.1038/emboj.2012.7
• Primary Citation of Related Structures:  
  4DGW


• PubMed Abstract: 
  

  SF3a is an evolutionarily conserved heterotrimeric complex essential for pre-mRNA splicing. It functions in spliceosome assembly within the mature U2 snRNP (small nuclear ribonucleoprotein particle), and its displacement from the spliceosome initiates the first step of the splicing reaction. We have identified a core domain of the yeast SF3a complex required for complex assembly and determined its crystal structure. The structure shows a bifurcated assembly of three subunits, Prp9, Prp11 and Prp21, with Prp9 interacting with Prp21 via a bidentate-binding mode, and Prp21 wrapping around Prp11. Structure-guided biochemical analysis also shows that Prp9 harbours a major binding site for stem-loop IIa of U2 snRNA. These findings provide mechanistic insights into the assembly of U2 snRNP.

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Organizational Affiliation: 

Structural Biology Program, The Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, and the Department of Pharmacology, New York University School of Medicine, New York, NY, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 89.73 kDa 
• Atom Count: 5,195 
• Modelled Residue Count: 633 
• Deposited Residue Count: 785 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pre-mRNA-splicing factor PRP9	A	402	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P19736 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P19736  Go to UniProtKB:  P19736

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pre-mRNA-splicing factor PRP21	B	152	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P32524 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32524  Go to UniProtKB:  P32524

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Pre-mRNA-splicing factor PRP11	C	231	Saccharomyces cerevisiae S288C	Mutation(s): 1
UniProt
Find proteins for Q07350 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q07350  Go to UniProtKB:  Q07350

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.11 Å
• R-Value Free: 0.278 
• R-Value Work: 0.228 
• R-Value Observed: 0.233 
• Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.781	α = 90
b = 127.259	β = 90
c = 169.173	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-02 
Deposition Author(s): Lin, P.C.

Revision History  

• Version 1.0: 2012-05-02
  Type: Initial release
  
• Version 1.1: 2018-07-25
  Changes: Data collection, Source and taxonomy, Structure summary