ISDA

Deposition Date 2022-10-09

Release Date 2023-10-04

Last Version Date 2024-11-20

Entry Detail

PDB ID:

8H40

Keywords:

TRANSCRIPTION

Title:

Cryo-EM structure of the transcription activation complex NtcA-TAC

Biological Source:

Source Organism:

Anabaena (Taxon ID: 1163)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.60 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (125-MER)
Chain IDs:A (auth: 1)
Chain Length:125
Number of Molecules:1
Biological Source:Anabaena

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (125-MER)
Chain IDs:B (auth: 2)
Chain Length:125
Number of Molecules:1
Biological Source:Anabaena

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta
Gene (Uniprot):rpoB
Chain IDs:C (auth: A)
Chain Length:1132
Number of Molecules:1
Biological Source:Anabaena

UniProt ID:P22703 Pfam ID:PF04563, PF04561, PF04565, PF10385, PF00562, PF04560

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta'
Gene (Uniprot):rpoC2
Chain IDs:D (auth: B)
Chain Length:1350
Number of Molecules:1
Biological Source:Anabaena

UniProt ID:P22705 Pfam ID:PF04983, PF05000, PF04998

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit alpha
Gene (Uniprot):rpoA
Chain IDs:E (auth: C), F (auth: D)
Chain Length:236
Number of Molecules:2
Biological Source:Anabaena

UniProt ID:Q8YPK3 Pfam ID:PF01193, PF01000

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit gamma
Gene (Uniprot):rpoC1
Chain IDs:G (auth: E)
Chain Length:625
Number of Molecules:1
Biological Source:Anabaena

UniProt ID:P22704 Pfam ID:PF04997, PF00623, PF04983

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit omega
Gene (Uniprot):rpoZ
Chain IDs:H (auth: F)
Chain Length:78
Number of Molecules:1
Biological Source:Anabaena

UniProt ID:Q8YNB9 Pfam ID:PF01192

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RNA polymerase sigma factor SigA
Gene (Uniprot):sigA
Chain IDs:I (auth: G)
Chain Length:390
Number of Molecules:1
Biological Source:Anabaena

UniProt ID:P26683 Pfam ID:PF00140, PF04542, PF04539, PF04545

Protein Blast

Polymer Type:polypeptide(L)
Molecule:NtcA
Gene (Uniprot):ntcA
Chain IDs:J (auth: X), K (auth: Y)
Chain Length:223
Number of Molecules:2
Biological Source:Anabaena

UniProt ID:P0A4U6 Pfam ID:PF00027, PF13545

Ligand Molecules

Primary Citation

DNA looping mediates cooperative transcription activation.

Han, S.J, Jiang, Y.L, You, L.L, Shen, L.Q, Wu, X, Yang, F, Cui, N, Kong, W.W, Sun, H, Zhou, K, Meng, H.C, Chen, Z.P, Chen, Y, Zhang, Y, Zhou, C.Z.Show

Nat.Struct.Mol.Biol. 31 293 299 (2024)

PMID: 38177666 DOI: 10.1038/s41594-023-01149-7

Abstact

Transcription factors respond to multilevel stimuli and co-occupy promoter regions of target genes to activate RNA polymerase (RNAP) in a cooperative manner. To decipher the molecular mechanism, here we report two cryo-electron microscopy structures of Anabaena transcription activation complexes (TACs): NtcA-TAC composed of RNAP holoenzyme, promoter and a global activator NtcA, and NtcA-NtcB-TAC comprising an extra context-specific regulator, NtcB. Structural analysis showed that NtcA binding makes the promoter DNA bend by ∼50°, which facilitates RNAP to contact NtcB at the distal upstream NtcB box. The sequential binding of NtcA and NtcB induces looping back of promoter DNA towards RNAP, enabling the assembly of a fully activated TAC bound with two activators. Together with biochemical assays, we propose a 'DNA looping' mechanism of cooperative transcription activation in bacteria.

Legend

Protein

Chemical

Disease

Primary Citation of related structures