5MS0

pseudo-atomic model of the RNA polymerase lambda-based antitermination complex solved by cryo-EM


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for lambda N-dependent processive transcription antitermination.

Said, N.Krupp, F.Anedchenko, E.Santos, K.F.Dybkov, O.Huang, Y.H.Lee, C.T.Loll, B.Behrmann, E.Burger, J.Mielke, T.Loerke, J.Urlaub, H.Spahn, C.M.T.Weber, G.Wahl, M.C.

(2017) Nat Microbiol 2: 17062-17062

  • DOI: 10.1038/nmicrobiol.2017.62
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • λN-mediated processive antitermination constitutes a paradigmatic transcription regulatory event, during which phage protein λN, host factors NusA, NusB, NusE and NusG, and an RNA nut site render elongating RNA polymerase termination-resistant. The s ...

    λN-mediated processive antitermination constitutes a paradigmatic transcription regulatory event, during which phage protein λN, host factors NusA, NusB, NusE and NusG, and an RNA nut site render elongating RNA polymerase termination-resistant. The structural basis of the process has so far remained elusive. Here we describe a crystal structure of a λN-NusA-NusB-NusE-nut site complex and an electron cryo-microscopic structure of a complete transcription antitermination complex, comprising RNA polymerase, DNA, nut site RNA, all Nus factors and λN, validated by crosslinking/mass spectrometry. Due to intrinsic disorder, λN can act as a multiprotein/RNA interaction hub, which, together with nut site RNA, arranges NusA, NusB and NusE into a triangular complex. This complex docks via the NusA N-terminal domain and the λN C-terminus next to the RNA exit channel on RNA polymerase. Based on the structures, comparative crosslinking analyses and structure-guided mutagenesis, we hypothesize that λN mounts a multipronged strategy to reprogram the transcriptional machinery, which may include (1) the λN C terminus clamping the RNA exit channel, thus stabilizing the DNA:RNA hybrid; (2) repositioning of NusA and RNAP elements, thus redirecting nascent RNA and sequestering the upstream branch of a terminator hairpin; and (3) hindering RNA engagement of termination factor ρ and/or obstructing ρ translocation on the transcript.


    Organizational Affiliation

    Microscopy and Cryo-Electron Microscopy Group, Max-Planck-Institut für Molekulare Genetik, Ihnestraße 63-73, D-14195 Berlin, Germany.,Institut für Klinische Chemie, Bioanalytik, Universitätsmedizin Göttingen, Robert-Koch-Straße 40, D-35075 Göttingen, Germany.,Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Straße 15, D-12489 Berlin, Germany.,Department of Cellular Biochemistry, Max Planck Institut für biophysikalische Chemie, Am Fassberg 11, D-37077 Göttingen, Germany.,Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, D-10117 Berlin, Germany.,Laboratory of Structural Biochemistry, Freie Universität Berlin, Takustraβe 6, D-14195 Berlin, Germany.,Bioanalytical Mass Spectrometry, Max Planck Institut für biophysikalische Chemie, Am Fassberg 11, D-37077 Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antitermination protein N
N
85Escherichia phage lambdaMutation(s): 0 
Gene Names: N
Find proteins for P03045 (Escherichia phage lambda)
Go to UniProtKB:  P03045
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
A, B
329Escherichia 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: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
C
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: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
D
1416Escherichia 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: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
E
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsJ (nusE)
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R5
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Transcription termination/antitermination protein NusG
F
183Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: nusG
Find proteins for P0AFG0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AFG0
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Transcription antitermination protein NusB
L
139Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: nusB (groNB, ssyB)
Find proteins for P0A780 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A780
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Transcription termination/antitermination protein NusA
M
497Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: nusA
Find proteins for P0AFF6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AFF6
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
O
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: 2
MoleculeChainsLengthOrganism
nascent RNAR29Escherichia coli
Entity ID: 8
MoleculeChainsLengthOrganism
RNA transcription bubbleH14Escherichia coli
Entity ID: 9
MoleculeChainsLengthOrganism
DNAII27Escherichia coli
Entity ID: 10
MoleculeChainsLengthOrganism
DNAIIJ39Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-12-29 
  • Released Date: 2017-05-03 
  • Deposition Author(s): Said, N., Krupp, F.

Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB740

Revision History 

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-05-10
    Type: Database references
  • Version 1.2: 2018-10-31
    Type: Author supporting evidence, Data collection, Database references, Source and taxonomy, Structure summary