Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 133.63 kDa 
• Atom Count: 9375 
• Residue Count: 856 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

5TF6

Structure and conformational plasticity of the U6 small nuclear ribonucleoprotein core

• DOI: 10.2210/pdb5TF6/pdb
• NDB: 5TF6

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


• Deposited: 2016-09-24 Released: 2017-01-11 
• Deposition Author(s): Montemayor, E.J., Brow, D.A., Butcher, S.E.
• 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: 2.30 Å
• R-Value Free: 0.232 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 

Literature

Structure and conformational plasticity of the U6 small nuclear ribonucleoprotein core.

Montemayor, E.J., Didychuk, A.L., Liao, H., Hu, P., Brow, D.A., Butcher, S.E.

(2017) Acta Crystallogr D Struct Biol 73: 1-8

• PubMed: 28045380 
• DOI: 10.1107/S2059798316018222
• Primary Citation of Related Structures:  
  5TF6


• PubMed Abstract: 
  

U6 small nuclear RNA (snRNA) is a key component of the active site of the spliceosome, a large ribonucleoprotein complex that catalyzes the splicing of precursor messenger RNA. Prior to its incorporation into the spliceosome, U6 is bound by the protein Prp24, which facilitates unwinding of the U6 internal stem-loop (ISL) so that it can pair with U4 snRNA. A previously reported crystal structure of the `core' of the U6 small nuclear ribonucleoprotein (snRNP) contained an ISL-stabilized A62G mutant of U6 bound to all four RNA-recognition motif (RRM) domains of Prp24 [Montemayor et al. (2014), Nature Struct. Mol. Biol. 21, 544-551]. The structure revealed a novel topology containing interlocked rings of protein and RNA that was not predicted by prior biochemical and genetic data. Here, the crystal structure of the U6 snRNP core with a wild-type ISL is reported. This complex crystallized in a new space group, apparently owing in part to the presence of an intramolecular cross-link in RRM1 that was not observed in the previously reported U6-A62G structure. The structure exhibits the same protein-RNA interface and maintains the unique interlocked topology. However, the orientation of the wild-type ISL is altered relative to the A62G mutant structure, suggesting inherent structural dynamics that may facilitate its pairing with U4. Consistent with their similar architectures in the crystalline state, the wild-type and A62G variants of U6 exhibit similar Prp24-binding affinities and electrophoretic mobilities when analyzed by gel-shift assay.

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Organizational Affiliation: 

Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
U4/U6 snRNA-associated-splicing factor PRP24	A, C	374	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: PRP24, YMR268C, YM8156.10C
Find proteins for P49960 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P49960  Go to UniProtKB:  P49960

Entity ID: 2
Molecule	Chains	Length	Organism	Image
U6 snRNA	B, D	72	Saccharomyces cerevisiae

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A, B, C	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	A, B, C, D	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	A, C	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.232 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.921	α = 90
b = 84.446	β = 90
c = 255.142	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-09-24 
• Released Date: 2017-01-11 
Deposition Author(s): Montemayor, E.J., Brow, D.A., Butcher, S.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM065166
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM118131
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM118075

Revision History 

• Version 1.0: 2017-01-11
  Type: Initial release
  
• Version 1.1: 2017-01-18
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence