PDBsum entry 2f3i

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protein links
Transferase PDB id
Protein chain
150 a.a. *
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Solution structure of a subunit of RNA polymerase ii
Structure: DNA-directed RNA polymerases i, ii, and iii 17.1 kda polypeptide. Chain: a. Synonym: RNA polymerase ii subunit, rpb17, rpb8, rpabc3. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 21 models
Authors: X.Kang,C.Jin
Key ref:
X.Kang et al. (2006). Structural, biochemical, and dynamic characterizations of the hRPB8 subunit of human RNA polymerases. J Biol Chem, 281, 18216-18226. PubMed id: 16632472 DOI: 10.1074/jbc.M513241200
21-Nov-05     Release date:   02-May-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P52434  (RPAB3_HUMAN) -  DNA-directed RNA polymerases I, II, and III subunit RPABC3
150 a.a.
150 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   7 terms 
  Biological process     viral reproduction   22 terms 
  Biochemical function     RNA polymerase I activity     5 terms  


DOI no: 10.1074/jbc.M513241200 J Biol Chem 281:18216-18226 (2006)
PubMed id: 16632472  
Structural, biochemical, and dynamic characterizations of the hRPB8 subunit of human RNA polymerases.
X.Kang, Y.Hu, Y.Li, X.Guo, X.Jiang, L.Lai, B.Xia, C.Jin.
The RPB8 subunit is present in all three types of eukaryotic RNA polymerases and is highly conserved during evolution. It is an essential subunit required for the transcription of nuclear genes, but the detailed mechanism including its interactions with different subunits and oligonucleotides remains largely unclear. Herein, we report the three-dimensional structure of human RPB8 (hRPB8) at high resolution determined by NMR spectroscopy. The protein fold comprises an eight-stranded beta-barrel, six short helices, and a large unstructured Omega-loop. The overall structure of hRPB8 is similar to that of yRPB8 from Saccharomyces cerevisiae and belongs to the oligonucleotide/oligosaccharide-binding fold. However, several features of the tertiary structures are notably different between the two proteins. In particular, hRPB8 has a more clustered positively charged binding interface with the largest subunit RPB1 of the RNA polymerases. We employed biochemical methods to detect its interactions with different single-stranded DNA sequences. In addition, single-stranded DNA titration experiments were performed to identify the residues involved in nonspecific binding with different DNA sequences. Furthermore, we characterized the millisecond time scale conformational flexibility of hRPB8 upon its binding to single-stranded DNA. The current results demonstrate that hRPB8 interacts with single-stranded DNA nonspecifically and adopts significant conformational changes, and the hRPB8/single-stranded DNA complex is a fast exchanging system. The solution structure in conjunction with the biochemical and dynamic studies reveal new aspects of this subunit in the molecular assembly and the biological function of the human nuclear RNA polymerases.
  Selected figure(s)  
Figure 4.
FIGURE 4. Solution structure of the hRPB8 subunit and its comparison with yRPB8. The superimposition of 20 representative structures with the lowest energy of hRPB8 are shown in A and B, and the orientations are with a 90° rotation. The ribbon diagrams of the mean structure of hRPB8 are shown in C and D with the secondary structural elements labeled. The orientations of C and D are related by a 90° rotation. The figures were generated using MOLMOL (30). E and F show the overlay of C^ trace of hRPB8 (blue) with that of yRPB8 (red, Protein Data Bank entry 1A1D). The unstructured -loop is not displayed in F for clarity.
Figure 8.
FIGURE 8. The millisecond time scale conformational exchanges of the hRPB8 subunit. A, the experimentally determined conformational exchanges (R[ex], normalized values) versus the amino acid sequence for the free hRPB8 are shown in black, and that of the hRPB8·ssDNA complex are shown in red. The spectra for determining the conformational exchanges (R[ex]) were recorded on a Bruker Avance 800 MHz spectrometer at 30 °C. The secondary structural elements are shown at the top. B-D, mapping of the conformational exchanges (R[ex]) onto the ribbon structure of hRPB8 for the free hRPB8 (B), hRPB8 binds with ssDNA with a ratio of 1.0:0.5 (C), and hRPB8 binds with ssDNA with a ratio of 1.0:1.5 (D). The residues showing conformational exchanges (R[ex]) on the millisecond time scale are represented with pink balls, and the missing residues are represented using gray balls.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 18216-18226) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21233849 F.Werner, and D.Grohmann (2011).
Evolution of multisubunit RNA polymerases in the three domains of life.
  Nat Rev Microbiol, 9, 85-98.  
19458260 H.Spåhr, G.Calero, D.A.Bushnell, and R.D.Kornberg (2009).
Schizosacharomyces pombe RNA polymerase II at 3.6-A resolution.
  Proc Natl Acad Sci U S A, 106, 9185-9190.
PDB code: 3h0g
19419240 Y.Korkhin, U.M.Unligil, O.Littlefield, P.J.Nelson, D.I.Stuart, P.B.Sigler, S.D.Bell, and N.G.Abrescia (2009).
Evolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure.
  PLoS Biol, 7, e102.
PDB codes: 2waq 2wb1
17697097 F.Werner (2007).
Structure and function of archaeal RNA polymerases.
  Mol Microbiol, 65, 1395-1404.  
18074396 R.L.Rich, and D.G.Myszka (2007).
Survey of the year 2006 commercial optical biosensor literature.
  J Mol Recognit, 20, 300-366.  
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 code is shown on the right.