5VSU

Structure of yeast U6 snRNP with 2'-phosphate terminated U6 RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.1 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
  • Structures With Same Primary Citation

  • 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 exte ...

    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 LengthOrganismDetails
U4/U6 snRNA-associated-splicing factor PRP24A452Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP24YMR268CYM8156.10C
Find proteins for P49960 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P49960
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm2B98Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM2SMX5SNP3YBL026WYBL0425
Find proteins for P38203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P38203
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm3C92Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM3SMX4USS2YLR438C-A
Find proteins for P57743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P57743
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm4D96Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM4SDB23USS1YER112W
Find proteins for P40070 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P40070
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm5E96Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM5YER146W
Find proteins for P40089 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm6F88Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM6YDR378CD9481.18
Find proteins for Q06406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q06406
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm7G118Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM7YNL147WN1202N1780
Find proteins for P53905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P53905
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
U6 snRNA-associated Sm-like protein LSm8H111Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LSM8YJR022WJ1464YJR83.16
Find proteins for P47093 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P47093
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  • Reference Sequence

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Entity ID: 9
MoleculeChainsLengthOrganism
Saccharomyces cerevisiae strain T8 chromosome XII sequenceI83Saccharomyces cerevisiae
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.157α = 90
b = 114.728β = 90
c = 179.844γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-05-12 
  • Released Date: 2018-05-09 
  • Deposition Author(s): Montemayor, E.J.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM065166
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 

  • Version 1.0: 2018-05-09
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence