8H3V image
Deposition Date 2022-10-09
Release Date 2023-10-04
Last Version Date 2024-10-30
Entry Detail
PDB ID:
8H3V
Keywords:
TRANSCRIPTION
Title:
Cryo-EM structure of the full transcription activation complex NtcA-NtcB-TAC
Biological Source:
Source Organism:
Anabaena (Taxon ID: 1163)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
4.50 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8H3V 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:NtcB
Gene (Uniprot):ntcB
Chain IDs:J (auth: S), K (auth: T), L (auth: U), M (auth: V)
Chain Length:312
Number of Molecules:4
Biological Source:Anabaena
UniProt ID:Q9L3R4 Pfam ID:PF00126, PF03466
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NtcA
Gene (Uniprot):ntcA
Chain IDs:N (auth: X), O (auth: Y)
Chain Length:223
Number of Molecules:2
Biological Source:Anabaena
UniProt ID:P0A4U6 Pfam ID:PF00027, PF13545
Ligand Molecules
NA
Primary Citation
DNA looping mediates cooperative transcription activation.
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.

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Primary Citation of related structures
8GZG
3LA2