6ASO

Structure of yeast U6 snRNP with 3'-phosphate terminated U6 RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Architecture of the U6 snRNP reveals specific recognition of 3'-end processed U6 snRNA.

Montemayor, E.J.Didychuk, A.L.Yake, A.D.Sidhu, G.K.Brow, D.A.Butcher, S.E.

(2018) Nat Commun 9: 1749-1749

  • DOI: 10.1038/s41467-018-04145-4
  • Primary Citation of Related Structures:  
    5VSU, 6ASO

  • PubMed Abstract: 
  • The spliceosome removes introns from precursor messenger RNA (pre-mRNA) to produce mature mRNA. Prior to catalysis, spliceosomes are assembled de novo onto pre-mRNA substrates. During this assembly process, U6 small nuclear RNA (snRNA) undergoes extensive structural remodeling ...

    The spliceosome removes introns from precursor messenger RNA (pre-mRNA) to produce mature mRNA. Prior to catalysis, spliceosomes are assembled de novo onto pre-mRNA substrates. During this assembly process, U6 small nuclear RNA (snRNA) undergoes extensive structural remodeling. The early stages of this remodeling process are chaperoned by U6 snRNP proteins Prp24 and the Lsm2-8 heteroheptameric ring. We now report a structure of the U6 snRNP from Saccharomyces cerevisiae. The structure reveals protein-protein contacts that position Lsm2-8 in close proximity to the chaperone "active site" of Prp24. The structure also shows how the Lsm2-8 ring specifically recognizes U6 snRNA that has been post-transcriptionally modified at its 3' end, thereby elucidating the mechanism by which U6 snRNPs selectively recruit 3' end-processed U6 snRNA into spliceosomes. Additionally, the structure reveals unanticipated homology between the C-terminal regions of Lsm8 and the cytoplasmic Lsm1 protein involved in mRNA decay.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA. sebutcher@wisc.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
U4/U6 snRNA-associated-splicing factor PRP24A424Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PRP24YMR268CYM8156.10C
UniProt
Find proteins for P49960 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm2B95Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: LSM2SMX5SNP3YBL026WYBL0425
UniProt
Find proteins for P38203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm3C97Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: LSM3SMX4USS2YLR438C-A
UniProt
Find proteins for P57743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm4D93Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: LSM4SDB23USS1YER112W
UniProt
Find proteins for P40070 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm5E93Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: LSM5YER146W
UniProt
Find proteins for P40089 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm6F88Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: LSM6SCY_1265
UniProt
Find proteins for A6ZYX7 (Saccharomyces cerevisiae (strain YJM789))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm7G115Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: LSM7YNL147WN1202N1780
UniProt
Find proteins for P53905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm8H115Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: LSM8YJR022WJ1464YJR83.16
UniProt
Find proteins for P47093 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsLengthOrganismImage
Saccharomyces cerevisiae strain HB_S_GIMBLETTROAD_9 chromosome XII sequenceI84Saccharomyces cerevisiae
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
K [auth I]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
J [auth A], L [auth I]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
M [auth I], N [auth I]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.197α = 90
b = 77.39β = 105.91
c = 118.614γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM118131
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM118075

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-09
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.2: 2020-10-21
    Changes: Data collection, Derived calculations