4NC8

N-terminal domain of delta-subunit of RNA polymerase complexed with nickel ions

Summary for 4NC8

• Entry DOI: 10.2210/pdb4nc8/pdb
• Related: 2KRC 4NC7
• Descriptor: DNA-directed RNA polymerase subunit delta, NICKEL (II) ION (3 entities in total)
• Functional Keywords: nucleus, transcription
• Biological source: Bacillus Subtilis
• Total number of polymer chains: 2
• Total formula weight: 23655.55

Authors

Demo, G.,Papouskova, V.,Komarek, J.,Sanderova, H.,Rabatinova, A.,Krasny, L.,Zidek, L.,Sklenar, V.,Wimmerova, M. (deposition date: 2013-10-24, release date: 2014-07-02, Last modification date: 2023-09-20)

Primary citation

Demo, G.,Papouskova, V.,Komarek, J.,Kaderavek, P.,Otrusinova, O.,Srb, P.,Rabatinova, A.,Krasny, L.,Zidek, L.,Sklenar, V.,Wimmerova, M.
X-ray vs. NMR structure of N-terminal domain of delta-subunit of RNA polymerase.
J.Struct.Biol., 187:174-186, 2014

PubMed Abstract: The crystal structure of the N-terminal domain of the RNA polymerase δ subunit (Nδ) from Bacillus subtilis solved at a resolution of 2.0Å is compared with the NMR structure determined previously. The molecule crystallizes in the space group C222(1) with a dimer in the asymmetric unit. Importantly, the X-ray structure exhibits significant differences from the lowest energy NMR structure. In addition to the overall structure differences, structurally important β sheets found in the NMR structure are not present in the crystal structure. We systematically investigated the cause of the discrepancies between the NMR and X-ray structures of Nδ, addressing the pH dependence, presence of metal ions, and crystal packing forces. We convincingly showed that the crystal packing forces, together with the presence of Ni(2+) ions, are the main reason for such a difference. In summary, the study illustrates that the two structural approaches may give unequal results, which need to be interpreted with care to obtain reliable structural information in terms of biological relevance.

PubMed: 24937760
DOI: 10.1016/j.jsb.2014.06.001

Experimental method

X-RAY DIFFRACTION (2.17 Å)