Macromolecule Content

• Total Structure Weight: 17.16 kDa 
• Atom Count: 1206 
• Residue Count: 150 
• Unique protein chains: 1

2F3I

Solution Structure of a Subunit of RNA Polymerase II

• DOI: 10.2210/pdb2F3I/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-11-21 Released: 2006-05-02 
• Deposition Author(s): Kang, X., Jin, C.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 21 
• Selection Criteria: structures with the lowest energy 

Literature

Structural, biochemical, and dynamic characterizations of the hRPB8 subunit of human RNA polymerases

Kang, X., Hu, Y., Li, Y., Guo, X., Jiang, X., Lai, L., Xia, B., Jin, C.

(2006) J Biol Chem 281: 18216-18226

• PubMed: 16632472 
• DOI: 10.1074/jbc.M513241200
• Primary Citation of Related Structures:  
  2F3I


• PubMed Abstract: 
  

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.

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Organizational Affiliation: 

Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III 17.1 kDa polypeptide	A	150	Homo sapiens	Mutation(s): 0  Gene Names: POLR2H EC: 2.7.7.6
Find proteins for P52434 (Homo sapiens) Explore P52434  Go to UniProtKB:  P52434
NIH Common Fund Data Resources
PHAROS:  P52434 GTEx:  ENSG00000163882

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 21 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2F3I Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-11-21 
• Released Date: 2006-05-02 
Deposition Author(s): Kang, X., Jin, C.

Revision History 

• Version 1.0: 2006-05-02
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance