5NSS image
Deposition Date 2017-04-26
Release Date 2017-06-28
Last Version Date 2025-07-02
Entry Detail
PDB ID:
5NSS
Keywords:
TRANSCRIPTION
Title:
Cryo-EM structure of RNA polymerase-sigma54 holoenzyme with promoter DNA and transcription activator PspF intermedate complex
Biological Source:
Source Organism:
Escherichia coli K-12 (Taxon ID: 83333)
Klebsiella pneumoniae (Taxon ID: 573)
Host Organism:
Escherichia coli BL21(DE3)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
5.80 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
5NSS validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit alpha
Gene (Uniprot):rpoA
Chain IDs:A, B
Chain Length:329
Number of Molecules:2
Biological Source:Escherichia coli K-12
UniProt ID:P0A7Z4 Pfam ID:PF01193, PF01000, PF03118 EC:2.7.7.6
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta
Gene (Uniprot):rpoB
Chain IDs:C
Chain Length:1342
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A8V2 Pfam ID:PF04563, PF04561, PF04565, PF10385, PF00562, PF04560 EC:2.7.7.6
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta',DNA-directed RNA polymerase subunit beta',DNA-directed RNA polymerase subunit beta'
Gene (Uniprot):rpoC
Chain IDs:D
Chain Length:1449
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A8T7 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998 EC:2.7.7.6
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit omega
Gene (Uniprot):rpoZ
Chain IDs:E
Chain Length:91
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A800 Pfam ID:PF01192 EC:2.7.7.6
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Psp operon transcriptional activator
Gene (Uniprot):pspF
Chain IDs:F, G, H (auth: J), I (auth: K), J (auth: L), K (auth: N)
Chain Length:295
Number of Molecules:6
Biological Source:Escherichia coli K-12
UniProt ID:P37344 Pfam ID:PF00158
Polymer Type:polydeoxyribonucleotide
Molecule:Non-template promoter DNA
Chain IDs:L (auth: H)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polydeoxyribonucleotide
Molecule:Template promoter DNA
Chain IDs:N (auth: I)
Chain Length:63
Number of Molecules:1
Biological Source:Klebsiella pneumoniae
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor RpoN,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor
Chain IDs:M
Chain Length:581
Number of Molecules:1
Biological Source:Klebsiella pneumoniae
UniProt ID:P06223 Pfam ID:PF00309, PF04963, PF04552
Ligand Molecules
NA
Primary Citation
Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation.
Mol. Cell 67 106 116.e4 (2017)
PMID: 28579332 DOI: 10.1016/j.molcel.2017.05.010

Abstact

Gene transcription is carried out by RNA polymerases (RNAPs). For transcription to occur, the closed promoter complex (RPc), where DNA is double stranded, must isomerize into an open promoter complex (RPo), where the DNA is melted out into a transcription bubble and the single-stranded template DNA is delivered to the RNAP active site. Using a bacterial RNAP containing the alternative σ54 factor and cryoelectron microscopy, we determined structures of RPc and the activator-bound intermediate complex en route to RPo at 3.8 and 5.8 Å. Our structures show how RNAP-σ54 interacts with promoter DNA to initiate the DNA distortions required for transcription bubble formation, and how the activator interacts with RPc, leading to significant conformational changes in RNAP and σ54 that promote RPo formation. We propose that DNA melting is an active process initiated in RPc and that the RNAP conformations of intermediates are significantly different from that of RPc and RPo.

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Primary Citation of related structures
5NSS