PDBsum entry 6bjs

Transcription/DNA/RNA

PDB id: 6bjs

Contents

Protein chains

222 a.a.

1316 a.a.

1337 a.a.

79 a.a.

DNA/RNA

Metals

_ZN ×2

_MG

PDB id:

6bjs

Name:

Transcription/DNA/RNA

Title:

Cryoem structure of e.Coli his pause elongation complex without pause hairpin

Structure:

DNA (32-mer). Chain: a. Engineered: yes. DNA (32-mer). Chain: b. Engineered: yes. RNA (29-mer). Chain: r. Engineered: yes.

Source:

Synthetic: yes. Salmonella enterica subsp. Enterica serovar typhimurium. Organism_taxid: 90371. Escherichia coli (strain k12). Organism_taxid: 83333. Strain: k12. Gene: rpoa, pez, phs, sez, b3295, jw3257. Expressed in: escherichia coli.

Authors:

J.Y.Kang,R.Landick,S.A.Darst

Key ref:

J.Y.Kang et al. (2018). RNA Polymerase Accommodates a Pause RNA Hairpin by Global Conformational Rearrangements that Prolong Pausing. Mol Cell, 69, 802. PubMed id: 29499135 DOI: 10.1016/j.molcel.2018.01.018

Date:

06-Nov-17 Release date: 28-Mar-18

Protein chains

P0A7Z4  (RPOA_ECOLI) -  DNA-directed RNA polymerase subunit alpha from Escherichia coli (strain K12)

Seq: 329 a.a.

Struc: 222 a.a.*

Protein chain

P0A8V2  (RPOB_ECOLI) -  DNA-directed RNA polymerase subunit beta from Escherichia coli (strain K12)

Seq: 1342 a.a.

Struc: 1316 a.a.

Protein chain

P0A8T7  (RPOC_ECOLI) -  DNA-directed RNA polymerase subunit beta' from Escherichia coli (strain K12)

Seq: 1407 a.a.

Struc: 1337 a.a.

Protein chain

P0A800  (RPOZ_ECOLI) -  DNA-directed RNA polymerase subunit omega from Escherichia coli (strain K12)

Seq: 91 a.a.

Struc: 79 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

C-G-T-C-C-T-T-C-G-G-A-A-G-A-G-A-T-T-C-A-G-A-G 23 bases

C-T-C-T-G-A-A-T-C-T-C-T-T-C-C-A-G-C-A-C-A-C-A-T-C-A-G-G-A-C-G 31 bases

C-G-A-U-G-U-G-U-G-C-U 11 bases

Enzyme reactions

• Enzyme class: Chains G, H, I, J, K: E.C.2.7.7.6 - DNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/j.molcel.2018.01.018

Mol Cell 69:802 (2018)

PubMed id: 29499135

RNA Polymerase Accommodates a Pause RNA Hairpin by Global Conformational Rearrangements that Prolong Pausing.

J.Y.Kang, T.V.Mishanina, M.J.Bellecourt, R.A.Mooney, S.A.Darst, R.Landick.

ABSTRACT

Sequence-specific pausing by RNA polymerase (RNAP) during transcription plays crucial and diverse roles in gene expression. In bacteria, RNA structures are thought to fold within the RNA exit channel of the RNAP and can increase pause lifetimes significantly. The biophysical mechanism of pausing is uncertain. We used single-particle cryo-EM to determine structures of paused complexes, including a 3.8-Å structure of an RNA hairpin-stabilized, paused RNAP that coordinates RNA folding in the his operon attenuation control region of E. coli. The structures revealed a half-translocated pause state (RNA post-translocated, DNA pre-translocated) that can explain transcriptional pausing and a global conformational change of RNAP that allosterically inhibits trigger loop folding and can explain pause hairpin action. Pause hairpin interactions with the RNAP RNA exit channel suggest how RNAP guides the formation of nascent RNA structures.