CID of human RPRD1B in complex with an unmodified CTD peptide

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


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.

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, D, E
135Homo sapiensMutation(s): 0 
Gene Names: RPRD1BC20orf77CREPT
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQG5 (Homo sapiens)
Explore Q9NQG5 
Go to UniProtKB:  Q9NQG5
GTEx:  ENSG00000101413 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NQG5
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
C, F
21N/AMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
FA [auth E],
P [auth B],
X [auth D],
Y [auth D]
O4 S
Query on UNX

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
CA [auth E]
DA [auth E]
EA [auth E]
AA [auth E],
BA [auth E],
CA [auth E],
DA [auth E],
EA [auth E],
G [auth A],
GA [auth F],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth B],
Q [auth D],
R [auth D],
S [auth D],
T [auth D],
U [auth D],
V [auth D],
W [auth D],
Z [auth E]
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.653α = 90
b = 134.707β = 106.64
c = 55.706γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-04
    Type: Initial release
  • Version 1.1: 2014-07-30
    Changes: Database references
  • Version 1.2: 2014-08-20
    Changes: Database references