9B9L | pdb_00009b9l

RPRD1B C-terminal interacting domain bound to a pThr4 CTD peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.347 (Depositor), 0.350 (DCC) 
  • R-Value Work: 
    0.266 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 
    0.274 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Thr 4 phosphorylation on RNA Pol II occurs at early transcription regulating 3'-end processing.

Moreno, R.Y.Panina, S.B.Irani, S.Hardtke, H.A.Stephenson, R.Floyd, B.M.Marcotte, E.M.Zhang, Q.Zhang, Y.J.

(2024) Sci Adv 10: eadq0350-eadq0350

  • DOI: https://doi.org/10.1126/sciadv.adq0350
  • Primary Citation of Related Structures:  
    9B9L

  • PubMed Abstract: 

    RNA polymerase II relies on a repetitive sequence domain (YSPTSPS) within its largest subunit to orchestrate transcription. While phosphorylation on serine-2/serine-5 of the carboxyl-terminal heptad repeats is well established, threonine-4's role remains enigmatic. Paradoxically, threonine-4 phosphorylation was only detected after transcription end sites despite functionally implicated in pausing, elongation, termination, and messenger RNA processing. Our investigation revealed that threonine-4 phosphorylation detection was obstructed by flanking serine-5 phosphorylation at the onset of transcription, which can be removed selectively. Subsequent proteomic analyses identified many proteins recruited to transcription via threonine-4 phosphorylation, which previously were attributed to serine-2. Loss of threonine-4 phosphorylation greatly reduces serine-2 phosphorylation, revealing a cross-talk between the two marks. Last, the function analysis of the threonine-4 phosphorylation highlighted its role in alternative 3'-end processing within pro-proliferative genes. Our findings unveil the true genomic location of this evolutionarily conserved phosphorylation mark and prompt a reassessment of functional assignments of the carboxyl-terminal domain.


  • Organizational Affiliation

    Department of Molecular Biosciences, University of Texas, Austin, TX, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Regulation of nuclear pre-mRNA domain-containing protein 1B
A, B
131Homo sapiensMutation(s): 0 
Gene Names: RPRD1BC20orf77CREPT
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQG5 (Homo sapiens)
Explore Q9NQG5 
Go to UniProtKB:  Q9NQG5
PHAROS:  Q9NQG5
GTEx:  ENSG00000101413 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NQG5
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SER-PRO-THR-SER-PRO-SER-TYR-SER-PRO-TPO-SER-PRO-SER-TYR-SER15Homo sapiensMutation(s): 0 
EC: 3.1.13 (UniProt), 2.7.7.48 (UniProt), 2.7.7.6 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P24928 (Homo sapiens)
Explore P24928 
Go to UniProtKB:  P24928
PHAROS:  P24928
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24928
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
C
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.347 (Depositor), 0.350 (DCC) 
  • R-Value Work:  0.266 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 0.274 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.317α = 90
b = 90.231β = 90
c = 135.074γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM-104896

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-07
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Structure summary
  • Version 1.2: 2025-02-19
    Changes: Database references