6GFW

Cryo-EM structure of bacterial RNA polymerase-sigma54 holoenzyme initial transcribing complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Structures of Bacterial RNA Polymerase Complexes Reveal the Mechanism of DNA Loading and Transcription Initiation.

Glyde, R., Ye, F., Jovanovic, M., Kotta-Loizou, I., Buck, M., Zhang, X.

(2018) Mol Cell 70: 1111-1120.e3

  • DOI: https://doi.org/10.1016/j.molcel.2018.05.021
  • Primary Citation of Related Structures:  
    6GFW, 6GH5, 6GH6

  • PubMed Abstract: 

    • Gene transcription is carried out by multi-subunit RNA polymerases (RNAPs). Transcription initiation is a dynamic multi-step process that involves the opening of the double-stranded DNA to form a transcription bubble and delivery of the template strand deep into the RNAP for RNA synthesis ...

    Gene transcription is carried out by multi-subunit RNA polymerases (RNAPs). Transcription initiation is a dynamic multi-step process that involves the opening of the double-stranded DNA to form a transcription bubble and delivery of the template strand deep into the RNAP for RNA synthesis. Applying cryoelectron microscopy to a unique transcription system using σ 54 (σ N ), the major bacterial variant sigma factor, we capture a new intermediate state at 4.1 Å where promoter DNA is caught at the entrance of the RNAP cleft. Combining with new structures of the open promoter complex and an initial de novo transcribing complex at 3.4 and 3.7 Å, respectively, our studies reveal the dynamics of DNA loading and mechanism of transcription bubble stabilization that involves coordinated, large-scale conformational changes of the universally conserved features within RNAP and DNA. In addition, our studies reveal a novel mechanism of strand separation by σ 54 .

    Organizational Affiliation: 

    Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK. Electronic address: xiaodong.zhang@imperial.ac.uk.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, B
329Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoA, pez, phs, sez, b3295, JW3257
EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
Explore P0A7Z4 
Go to UniProtKB:  P0A7Z4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7Z4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,342Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950
EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12))
Explore P0A8V2 
Go to UniProtKB:  P0A8V2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8V2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'1,407Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoC, tabB, b3988, JW3951
EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12))
Explore P0A8T7 
Go to UniProtKB:  P0A8T7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8T7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega91Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoZ, b3649, JW3624
EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12))
Explore P0A800 
Go to UniProtKB:  P0A800
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A800
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma-54 factorH [auth M]497Klebsiella pneumoniaeMutation(s): 1 
Gene Names: SM87_03359, CP995_28845
EC: 2.7.7.6
UniProt
Find proteins for P06223 (Klebsiella oxytoca)
Explore P06223 
Go to UniProtKB:  P06223
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06223
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsLengthOrganismImage
nifH promoter template DNA63Klebsiella pneumoniae
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsLengthOrganismImage
NifH promoter non-template DNA63Klebsiella pneumoniae
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 8
MoleculeChainsLengthOrganismImage
de novo synthesized RNAI [auth R]4Escherichia coli K-12
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.10.1
MODEL REFINEMENTCCP4 package7

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/N007816

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-04
    Type: Initial release