PDBsum entry 3d9i

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Transcription PDB id
Protein chains
138 a.a. *
SO4 ×11
NH4 ×6
GOL ×4
Waters ×190
* Residue conservation analysis
PDB id:
Name: Transcription
Title: Snapshots of the RNA processing factor scaf8 bound to differ phosphorylated forms of the carboxy-terminal domain of RNA- ii
Structure: RNA-binding protein 16. Chain: a, b. Fragment: ctd interacting domain of scaf8, unp residues 1-1 synonym: RNA-binding motif protein 16. Engineered: yes. Mutation: yes
Source: Homo sapiens. Man. Organism_taxid: 9606. Gene: rbm16, kiaa1116. Expressed in: escherichia coli.
1.91Å     R-factor:   0.183     R-free:   0.216
Authors: R.Becker,B.Loll,A.Meinhart
Key ref:
R.Becker et al. (2008). Snapshots of the RNA Processing Factor SCAF8 Bound to Different Phosphorylated Forms of the Carboxyl-terminal Domain of RNA Polymerase II. J Biol Chem, 283, 22659-22669. PubMed id: 18550522 DOI: 10.1074/jbc.M803540200
27-May-08     Release date:   10-Jun-08    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q9UPN6  (SCAF8_HUMAN) -  Protein SCAF8
1271 a.a.
138 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)


DOI no: 10.1074/jbc.M803540200 J Biol Chem 283:22659-22669 (2008)
PubMed id: 18550522  
Snapshots of the RNA Processing Factor SCAF8 Bound to Different Phosphorylated Forms of the Carboxyl-terminal Domain of RNA Polymerase II.
R.Becker, B.Loll, A.Meinhart.
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.
  Selected figure(s)  
Figure 1.
FIGURE 1. SCAF8-CID binding to different phosphorylated forms of the CTD measured by fluorescence anisotropy competition titration experiments. Data points of the reference measurement of SCAF8-CID titrated to 2 µM FAM-Ser(P)-2-CTD peptide are presented as filled circles ( ). Data points for competition experiments where 100 µM concentrations of different non-fluorescently labeled CTD peptides competed against 2 µM FAM-Ser(P)-2-CTD peptide are given as open symbols. Fluorescence anisotropy data using Ser(P)-2/Ser(P)-5-CTD peptide are presented as open diamonds ( ) (K[d] = 19 (+/- 2/2) µM), Ser(P)-2-CTD peptide as open circles ( ) (K[d] = 68 (+/- 8/6) µM), Ser(P)-2/Ser(P)-7-CTD as open squares ( ) (K[d] = 90 (+/- 4/3) µM), and Ser(P)-5-CTD as inverted open triangles ( ) (K[d] = 330 (+/- 50/30) µM). The lines represent the best fit to data of individual measurements.
Figure 3.
FIGURE 3. A gallery of SCAF8-CID binding to different phospho forms of the CTD. SCAF8-CID is shown as a ribbon representation; the CTD is shown as a stick model. Hydrogen bonds between SCAF8-CID and the CTD are illustrated as black dashed lines, and intramolecular hydrogen bonds within the β-turn of the CTD are in orange. 2F[o] - F[c] electron density contoured at 0.9 for the bound CTD-peptides is illustrated beneath each model. Shown is SCAF8-CID binding Ser(P)-2/Ser(P)-5-CTD (PDB code 3D9K) (A), Ser(P)-2-CTD (PDB code 3D9L) (B), Ser(P)-5-CTD (PDB code 3D9M) (C), unphosphorylated CTD (PDB code 3D9O) (D), and Ser(P)-2/Ser(P)-7-CTD (PDB code 3D9N) (E) and Pcf11-CID (PDB code 1SZA) binding Ser(P)-2-CTD (F).
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 22659-22669) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20818393 B.M.Lunde, S.L.Reichow, M.Kim, H.Suh, T.C.Leeper, F.Yang, H.Mutschler, S.Buratowski, A.Meinhart, and G.Varani (2010).
Cooperative interaction of transcription termination factors with the RNA polymerase II C-terminal domain.
  Nat Struct Mol Biol, 17, 1195-1201.
PDB codes: 2km4 2l0i
21094070 S.M.McDonald, D.Close, H.Xin, T.Formosa, and C.P.Hill (2010).
Structure and biological importance of the Spn1-Spt6 interaction, and its regulatory role in nucleosome binding.
  Mol Cell, 40, 725-735.
PDB codes: 3o8z 3oak
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.