3D9L

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

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: 10.1074/jbc.M803540200
  • Primary Citation of Related Structures:  

  • 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 recruitmen ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-binding protein 16
A, B
145Homo sapiensMutation(s): 0 
Gene Names: SCAF8 (CCAP7, KIAA1116, RBM16)
Find proteins for Q9UPN6 (Homo sapiens)
Go to Gene View: SCAF8
Go to UniProtKB:  Q9UPN6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CTD-PEPTIDE
Y, Z
15Homo sapiensMutation(s): 0 
Gene Names: POLR2A (POLR2)
EC: 2.7.7.6
Find proteins for P24928 (Homo sapiens)
Go to Gene View: POLR2A
Go to UniProtKB:  P24928
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT
Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
Y, Z
L-PEPTIDE LINKINGC3 H8 N O6 PSER
BTN
Query on BTN
Y, Z
NON-POLYMERC10 H16 N2 O3 S

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.188 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 56.296α = 90.00
b = 56.296β = 90.00
c = 106.739γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
XSCALEdata scaling
XDSdata reduction
REFMACrefinement
MAR345data collection

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-06-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description