4FLB

CID of human RPRD2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

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 2144Homo sapiensMutation(s): 0 
Gene Names: RPRD2KIAA0460HSPC099
UniProt & NIH Common Fund Data Resources
Find proteins for Q5VT52 (Homo sapiens)
Explore Q5VT52 
Go to UniProtKB:  Q5VT52
PHAROS:  Q5VT52
GTEx:  ENSG00000163125 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5VT52
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PR
Query on PR

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
PRASEODYMIUM ION
Pr
WCWKKSOQLQEJTE-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
UNX
Query on UNX

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
UNKNOWN ATOM OR ION
X
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.339α = 90
b = 40.339β = 90
c = 145.75γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2014-06-11
    Changes: Structure summary
  • Version 1.2: 2014-07-30
    Changes: Database references
  • Version 1.3: 2014-08-20
    Changes: Database references
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references, Derived calculations