7BEG

Structures of class I bacterial transcription complexes


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of Class I and Class II Transcription Complexes Reveal the Molecular Basis of RamA-Dependent Transcription Activation.

Hao, M.Ye, F.Jovanovic, M.Kotta-Loizou, I.Xu, Q.Qin, X.Buck, M.Zhang, X.Wang, M.

(2022) Adv Sci (Weinh) 9: e2103669-e2103669

  • DOI: https://doi.org/10.1002/advs.202103669
  • Primary Citation of Related Structures:  
    7BEF, 7BEG

  • PubMed Abstract: 

    Transcription activator RamA is linked to multidrug resistance of Klebsiella pneumoniae through controlling genes that encode efflux pumps (acrA) and porin-regulating antisense RNA (micF). In bacteria, σ 70 , together with activators, controls the majority of genes by recruiting RNA polymerase (RNAP) to the promoter regions. RNAP and σ 70 form a holoenzyme that recognizes -35 and -10 promoter DNA consensus sites. Many activators bind upstream from the holoenzyme and can be broadly divided into two classes. RamA acts as a class I activator on acrA and class II activator on micF, respectively. The authors present biochemical and structural data on RamA in complex with RNAP-σ 70 at the two promoters and the data reveal the molecular basis for how RamA assembles and interacts with core RNAP and activates transcription that contributes to antibiotic resistance. Further, comparing with CAP/TAP complexes reveals common and activator-specific features in activator binding and uncovers distinct roles of the two C-terminal domains of RNAP α subunit.


  • Organizational Affiliation

    Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, 200040, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, B
329Escherichia coliMutation(s): 0 
Gene Names: rpoApezphssezb3295JW3257
EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
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UniProt GroupP0A7Z4
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,342Escherichia coliMutation(s): 0 
Gene Names: rpoBZ5560ECs4910
EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12))
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UniProt GroupP0A8V2
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'1,407Escherichia coliMutation(s): 0 
Gene Names: rpoCZ5561ECs4911
EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12))
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UniProt GroupP0A8T7
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega91Escherichia coliMutation(s): 0 
Gene Names: rpoZb3649JW3624
EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12))
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UniProt GroupP0A800
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoD630Escherichia coliMutation(s): 0 
Gene Names: rpoDGHR40_08205NCTC12650_00972
UniProt
Find proteins for P00579 (Escherichia coli (strain K12))
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UniProt GroupP00579
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional activator RamAI [auth G]130Klebsiella pneumoniaeMutation(s): 0 
Gene Names: ramA
UniProt
Find proteins for Q48413 (Klebsiella pneumoniae)
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UniProt GroupQ48413
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Entity ID: 6
MoleculeChains LengthOrganismImage
Class I pacrA promoter non-template DNAG [auth N]94Klebsiella pneumoniae
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Entity ID: 7
MoleculeChains LengthOrganismImage
Class I pacrA promoter template DNAH [auth T]94Klebsiella pneumoniae
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot
MODEL REFINEMENTPHENIX
MODEL REFINEMENTREFMAC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)ChinaBB/N007816/1
Medical Research Council (MRC, United Kingdom)ChinaMR/P007503/1
National Science Foundation (NSF, China)China81991531

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-01
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2024-07-10
    Changes: Data collection, Refinement description