8QSZ | pdb_00008qsz

Structure of s. pombe RNA polymerase II in complex with DSIF and Rat1/Rai1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.67 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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This is version 1.2 of the entry. See complete history


Literature

DSIF factor Spt5 coordinates transcription, maturation and exoribonucleolysis of RNA polymerase II transcripts.

Kus, K.Carrique, L.Kecman, T.Fournier, M.Hassanein, S.S.Aydin, E.Kilchert, C.Grimes, J.M.Vasiljeva, L.

(2025) Nat Commun 16: 10-10

  • DOI: https://doi.org/10.1038/s41467-024-55063-7
  • Primary Citation of Related Structures:  
    8QSZ

  • PubMed Abstract: 

    Precursor messenger RNA (pre-mRNA) is processed into its functional form during RNA polymerase II (Pol II) transcription. Although functional coupling between transcription and pre-mRNA processing is established, the underlying mechanisms are not fully understood. We show that the key transcription termination factor, RNA exonuclease Xrn2 engages with Pol II forming a stable complex. Xrn2 activity is stimulated by Spt5 to ensure efficient degradation of nascent RNA leading to Pol II dislodgement from DNA. Our results support a model where Xrn2 first forms a stable complex with the elongating Pol II to achieve its full activity in degrading nascent RNA revising the current 'torpedo' model of termination, which posits that RNA degradation precedes Xrn2 engagement with Pol II. Spt5 is also a key factor that attenuates the expression of non-coding transcripts, coordinates pre-mRNA splicing and 3'-end processing. Our findings indicate that engagement with the transcribing Pol II is an essential regulatory step modulating the activity of RNA enzymes such as Xrn2, thus advancing our understanding of how RNA maturation is controlled during transcription.


  • Organizational Affiliation
    • Department of Biochemistry, University of Oxford, Oxford, United Kingdom. krzysztof.kus@bioch.ox.ac.uk.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit rpb11,752Schizosaccharomyces pombeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P36594 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB21,210Schizosaccharomyces pombeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q02061 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3297Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P37382 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1D [auth E]210Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2E [auth F]142Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit rpb7F [auth G]172Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3G [auth H]125Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9,RBP9H [auth I]141Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5I [auth J]71Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11J [auth K]123Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC4K [auth L]63Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor spt5L [auth Y]1,122Schizosaccharomyces pombeMutation(s): 0 
Gene Names: spt5
UniProt
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UniProt GroupO13936
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
5'-3' exoribonuclease 2P [auth X]896Schizosaccharomyces pombeMutation(s): 0 
Gene Names: dhp1
EC: 3.1.13
UniProt
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Entity ID: 13
MoleculeChains LengthOrganismImage
DNA none template (34-MER)M [auth N]48Schizosaccharomyces pombe
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Entity ID: 14
MoleculeChains LengthOrganismImage
RNA (5'-R(P*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3')N [auth P]26Schizosaccharomyces pombe
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Entity ID: 15
MoleculeChains LengthOrganismImage
DNA template (40-MER)O [auth T]48Schizosaccharomyces pombe
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
Q [auth C]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.67 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCV3.8
MODEL REFINEMENTCoot0.9.8.7
MODEL REFINEMENTPHENIX1.20

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom200835/Z/16/Z
Wellcome TrustUnited Kingdom222510/Z/21/Z
Wellcome TrustUnited KingdomWT106994/Z/15/Z
Wellcome TrustUnited Kingdom093305/Z/10/Z
Wellcome TrustUnited Kingdom060208/Z/00/Z
Wellcome TrustUnited Kingdom203141/Z/16/Z

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-23
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection
  • Version 1.2: 2025-01-22
    Changes: Data collection, Database references