6FLQ

CryoEM structure of E.coli RNA polymerase paused elongation complex bound to NusA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Basis for NusA Stabilized Transcriptional Pausing.

Guo, X.Myasnikov, A.G.Chen, J.Crucifix, C.Papai, G.Takacs, M.Schultz, P.Weixlbaumer, A.

(2018) Mol Cell 69: 816-827.e4

  • DOI: 10.1016/j.molcel.2018.02.008
  • Primary Citation of Related Structures:  
    6FLQ, 6FLP

  • PubMed Abstract: 
  • Transcriptional pausing by RNA polymerases (RNAPs) is a key mechanism to regulate gene expression in all kingdoms of life and is a prerequisite for transcription termination. The essential bacterial transcription factor NusA stimulates both pausing a ...

    Transcriptional pausing by RNA polymerases (RNAPs) is a key mechanism to regulate gene expression in all kingdoms of life and is a prerequisite for transcription termination. The essential bacterial transcription factor NusA stimulates both pausing and termination of transcription, thus playing a central role. Here, we report single-particle electron cryo-microscopy reconstructions of NusA bound to paused E. coli RNAP elongation complexes with and without a pause-enhancing hairpin in the RNA exit channel. The structures reveal four interactions between NusA and RNAP that suggest how NusA stimulates RNA folding, pausing, and termination. An asymmetric translocation intermediate of RNA and DNA converts the active site of the enzyme into an inactive state, providing a structural explanation for the inhibition of catalysis. Comparing RNAP at different stages of pausing provides insights on the dynamic nature of the process and the role of NusA as a regulatory factor.


    Organizational Affiliation

    Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch Cedex, France; Université de Strasbourg, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale (Inserm), U964, 67404 Illkirch Cedex, France. Electronic address: albert.weixlbaumer@igbmc.fr.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaAB329Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoApezphssezb3295JW3257
EC: 2.7.7.6
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A7Z4
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC1342Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoBgroNnitBrifronstlstvtabDb3987JW3950
EC: 2.7.7.6
Find proteins for P0A8V2 (Escherichia coli (strain K12))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D1407Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoCtabBb3988JW3951
EC: 2.7.7.6
Find proteins for P0A8T7 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A8T7
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE91Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoZb3649JW3624
EC: 2.7.7.6
Find proteins for P0A800 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription termination/antitermination protein NusAF495Escherichia coli K-12Mutation(s): 0 
Gene Names: nusAb3169JW3138
Find proteins for P0AFF6 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0AFF6
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (31-MER)N31synthetic construct
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Entity ID: 7
MoleculeChainsLengthOrganismImage
RNA (5'-R(*CP*CP*UP*GP*AP*UP*CP*AP*GP*GP*CP*GP*AP*UP*GP*UP*GP*UP*GP*CP*U)-3')R21synthetic construct
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Entity ID: 8
MoleculeChainsLengthOrganismImage
DNA (39-MER)T39synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilFranceERC starting grant 679734

Revision History 

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Other