4JXT

CID of human RPRD1A in complex with a phosphorylated peptide from RPB1-CTD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

RPRD1A and RPRD1B are human RNA polymerase II C-terminal domain scaffolds for Ser5 dephosphorylation.

Ni, Z.Xu, C.Guo, X.Hunter, G.O.Kuznetsova, O.V.Tempel, W.Marcon, E.Zhong, G.Guo, H.Kuo, W.H.Li, J.Young, P.Olsen, J.B.Wan, C.Loppnau, P.El Bakkouri, M.Senisterra, G.A.He, H.Huang, H.Sidhu, S.S.Emili, A.Murphy, S.Mosley, A.L.Arrowsmith, C.H.Min, J.Greenblatt, J.F.

(2014) Nat Struct Mol Biol 21: 686-695

  • DOI: https://doi.org/10.1038/nsmb.2853
  • Primary Citation of Related Structures:  
    4FLA, 4FLB, 4JXT, 4Q94, 4Q96

  • PubMed Abstract: 

    The RNA polymerase II (RNAPII) C-terminal domain (CTD) heptapeptide repeats (1-YSPTSPS-7) undergo dynamic phosphorylation and dephosphorylation during the transcription cycle to recruit factors that regulate transcription, RNA processing and chromatin modification. We show here that RPRD1A and RPRD1B form homodimers and heterodimers through their coiled-coil domains and interact preferentially via CTD-interaction domains (CIDs) with RNAPII CTD repeats phosphorylated at S2 and S7. Crystal structures of the RPRD1A, RPRD1B and RPRD2 CIDs, alone and in complex with RNAPII CTD phosphoisoforms, elucidate the molecular basis of CTD recognition. In an example of cross-talk between different CTD modifications, our data also indicate that RPRD1A and RPRD1B associate directly with RPAP2 phosphatase and, by interacting with CTD repeats where phospho-S2 and/or phospho-S7 bracket a phospho-S5 residue, serve as CTD scaffolds to coordinate the dephosphorylation of phospho-S5 by RPAP2.


  • Organizational Affiliation

    Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Regulation of nuclear pre-mRNA domain-containing protein 1A138Homo sapiensMutation(s): 0 
Gene Names: RPRD1AP15RS
UniProt & NIH Common Fund Data Resources
Find proteins for Q96P16 (Homo sapiens)
Explore Q96P16 
Go to UniProtKB:  Q96P16
PHAROS:  Q96P16
GTEx:  ENSG00000141425 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96P16
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB121Homo sapiensMutation(s): 1 
EC: 2.7.7.6 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 3.1.13 (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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: I 4
  • Diffraction Data: https://doi.org/10.18430/m34jxt
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.264α = 90
b = 93.264β = 90
c = 36.027γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-13
    Type: Initial release
  • Version 1.1: 2014-07-16
    Changes: Database references
  • Version 1.2: 2014-08-20
    Changes: Database references
  • Version 1.3: 2018-04-04
    Changes: Data collection
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description