Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the Carboxy-Terminal Domain of RNA-Polymerase II

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Snapshots of the RNA Processing Factor SCAF8 Bound to Different Phosphorylated Forms of the Carboxyl-terminal Domain of RNA Polymerase II.

Becker, R.Loll, B.Meinhart, A.

(2008) J Biol Chem 283: 22659-22669

  • DOI: https://doi.org/10.1074/jbc.M803540200
  • Primary Citation of Related Structures:  
    3D9I, 3D9J, 3D9K, 3D9L, 3D9M, 3D9N, 3D9O, 3D9P

  • PubMed Abstract: 

    Concomitant with RNA polymerase II (Pol II) transcription, RNA maturation factors are recruited to the carboxyl-terminal domain (CTD) of Pol II, whose phosphorylation state changes during a transcription cycle. CTD phosphorylation triggers recruitment of functionally different factors involved in RNA processing and transcription termination; most of these factors harbor a conserved CTD interacting domain (CID). Orchestration of factor recruitment is believed to be conducted by CID recognition of distinct phosphorylated forms of the CTD. We show that the human RNA processing factor SCAF8 interacts weakly with the unphosphorylated CTD of Pol II. Upon phosphorylation, affinity for the CTD is increased; however, SCAF8 is promiscuous to the phosphorylation pattern on the CTD. Employing a combined structural and biophysical approach, we were able to distinguish motifs within CIDs that are involved in a generic CTD sequence recognition from items that confer phospho-specificity.

  • Organizational Affiliation

    Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding protein 16
A, B
145Homo sapiensMutation(s): 0 
Gene Names: RBM16KIAA1116
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UPN6 (Homo sapiens)
Explore Q9UPN6 
Go to UniProtKB:  Q9UPN6
GTEx:  ENSG00000213079 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UPN6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth B]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
AA [auth B],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
X [auth B],
Y [auth B],
Z [auth B]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth B],
O [auth A],
P [auth A],
Q [auth A]
C3 H8 O3
Query on NH4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B]
H4 N
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.62α = 90
b = 57.62β = 90
c = 107.15γ = 90
Software Package:
Software NamePurpose
MAR345data collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description