PDBsum entry 7d7c

Transcription

PDB id: 7d7c

Contents

Protein chains

219 a.a.

1316 a.a.

1335 a.a.

137 a.a.

DNA/RNA

Metals

_ZN ×2

_MG

PDB id:

7d7c

Name:

Transcription

Title:

Cryoem structure of gp55-dependent RNA polymerase-promoter open complex

Structure:

DNA-directed RNA polymerase subunit alpha. Chain: a, b. Synonym: rnap subunit alpha,RNA polymerase subunit alpha, transcriptase subunit alpha. Engineered: yes. DNA-directed RNA polymerase subunit beta. Chain: c. Synonym: rnap subunit beta,RNA polymerase subunit beta,transcriptase subunit beta.

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Escherichia coli 1-392-07_s4_c3. Organism_taxid: 1444275. Gene: rpob, ad40_4833. Synthetic: yes. Organism_taxid: 562

Authors:

J.Shi,A.Wen,S.Jin,Y.Feng

Key ref:

J.Shi et al. (2021). Transcription activation by a sliding clamp. Nat Commun, 12, 1131. PubMed id: 33602900 DOI: 10.1038/s41467-021-21392-0

Date:

03-Oct-20 Release date: 20-Jan-21

Protein chains

U9ZUN7  (A0A080FHH4_ECOLX) -

Protein chain

A0A080FHH4  () -

Protein chain

D7Y6A2  (D7Y6A2_ECOLX) -

Protein chain

No UniProt id for this chain

Struc: 137 a.a.

DNA/RNA chains

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

A-G-A-G-T-A-T-A-A-A-G-A-T-A-C-T-G-A-A-G-C-A-G-C-C 25 bases

Enzyme reactions

• Enzyme class: Chains A, B, C, D: 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: 10.1038/s41467-021-21392-0

Nat Commun 12:1131 (2021)

PubMed id: 33602900

Transcription activation by a sliding clamp.

J.Shi, A.Wen, S.Jin, B.Gao, Y.Huang, Y.Feng.

ABSTRACT

Transcription activation of bacteriophage T4 late genes is accomplished by a transcription activation complex containing RNA polymerase (RNAP), the promoter specificity factor gp55, the coactivator gp33, and a universal component of cellular DNA replication, the sliding clamp gp45. Although genetic and biochemical studies have elucidated many aspects of T4 late gene transcription, no precise structure of the transcription machinery in the process is available. Here, we report the cryo-EM structures of a gp55-dependent RNAP-promoter open complex and an intact gp45-dependent transcription activation complex. The structures reveal the interactions between gp55 and the promoter DNA that mediate the recognition of T4 late promoters. In addition to the σR2 homology domain, gp55 has a helix-loop-helix motif that chaperons the template-strand single-stranded DNA of the transcription bubble. Gp33 contacts both RNAP and the upstream double-stranded DNA. Gp45 encircles the DNA and tethers RNAP to it, supporting the idea that gp45 switches the promoter search from three-dimensional diffusion mode to one-dimensional scanning mode.