6ALG

CryoEM structure of HK022 Nun - E.coli RNA polymerase elongation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Structural basis of transcription arrest by coliphage HK022 Nun in anEscherichia coliRNA polymerase elongation complex.

Kang, J.Y.Olinares, P.D.Chen, J.Campbell, E.A.Mustaev, A.Chait, B.T.Gottesman, M.E.Darst, S.A.

(2017) Elife 6: --

  • DOI: 10.7554/eLife.25478
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Coliphage HK022 Nun blocks superinfection by coliphage λ by stalling RNA polymerase (RNAP) translocation specifically on λ DNA. To provide a structural framework to understand how Nun blocks RNAP translocation, we determined structures of <i>Escheri ...

    Coliphage HK022 Nun blocks superinfection by coliphage λ by stalling RNA polymerase (RNAP) translocation specifically on λ DNA. To provide a structural framework to understand how Nun blocks RNAP translocation, we determined structures of Escherichia coli RNAP ternary elongation complexes (TECs) with and without Nun by single-particle cryo-electron microscopy. Nun fits tightly into the TEC by taking advantage of gaps between the RNAP and the nucleic acids. The C-terminal segment of Nun interacts with the RNAP β and β' subunits inside the RNAP active site cleft as well as with nearly every element of the nucleic acid scaffold, essentially crosslinking the RNAP and the nucleic acids to prevent translocation, a mechanism supported by the effects of Nun amino acid substitutions. The nature of Nun interactions inside the RNAP active site cleft suggests that RNAP clamp opening is required for Nun to establish its interactions, explaining why Nun acts on paused TECs.


    Organizational Affiliation

    Department of Microbiology and Molecular Genetics, Rutgers Biomedical and Health Sciences, Newark, United States.,Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York City, United States.,Laboratory of Molecular Biophysics, The Rockefeller University, New York City, United States.,Public Health Research Institute, Newark, United States.,Department of Microbiology and Immunology, Columbia University Medical Center, New York City, United States.,Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
G, H
239Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoA (pez, phs, sez)
EC: 2.7.7.6
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Z4
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
I
1342Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoB (groN, nitB, rif, ron, stl, stv, tabD)
EC: 2.7.7.6
Find proteins for P0A8V2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8V2
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
J
1407Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoC (tabB)
EC: 2.7.7.6
Find proteins for P0A8T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8T7
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
K
91Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for P0A800 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A800
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Transcription termination factor nun
N
109Escherichia phage HK022Mutation(s): 0 
Gene Names: nun
Find proteins for P18683 (Escherichia phage HK022)
Go to UniProtKB:  P18683
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (29-MER)A29Enterobacteria phage T7
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (29-MER)B29Enterobacteria phage T7
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(P*CP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')R20Enterobacteria phage T7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
J
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
J
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-08-07 
  • Released Date: 2017-08-16 
  • Deposition Author(s): Kang, J.Y., Darst, S.A.
  • This entry supersedes: 5UP6

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR35 GM118130

Revision History 

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence, Data collection
  • Version 1.2: 2017-11-08
    Type: Derived calculations
  • Version 1.3: 2018-02-28
    Type: Database references, Other
  • Version 1.4: 2018-03-28
    Type: Data collection, Database references
  • Version 1.5: 2018-07-18
    Type: Data collection