4Q94

human RPRD1B CID in complex with a RPB1-CTD derived Ser2 phosphorylated peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/nsmb.2853
  • Primary Citation of Related Structures:  

  • 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 chromati ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Regulation of nuclear pre-mRNA domain-containing protein 1B
A, B
135Homo sapiensMutation(s): 0 
Gene Names: RPRD1B (C20orf77, CREPT)
Find proteins for Q9NQG5 (Homo sapiens)
Go to Gene View: RPRD1B
Go to UniProtKB:  Q9NQG5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
rpb1-ctd
C, D
21N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
UNX
Query on UNX

Download SDF File 
Download CCD File 
A, B, C, D
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
C, D
NON-POLYMERH2 N

--

SEP
Query on SEP
C, D
L-PEPTIDE LINKINGC3 H8 N O6 PSER
BTN
Query on BTN
C, D
NON-POLYMERC10 H16 N2 O3 S

--

Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 39.286α = 90.00
b = 70.448β = 90.00
c = 108.859γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2014-07-30
    Type: Database references
  • Version 1.2: 2014-08-20
    Type: Database references