6PSV

Escherichia coli RNA polymerase promoter unwinding intermediate (TpreRPo) with TraR and rpsT P2 promoter


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 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

Stepwise Promoter Melting by Bacterial RNA Polymerase.

Chen, J.Chiu, C.Gopalkrishnan, S.Chen, A.Y.Olinares, P.D.B.Saecker, R.M.Winkelman, J.T.Maloney, M.F.Chait, B.T.Ross, W.Gourse, R.L.Campbell, E.A.Darst, S.A.

(2020) Mol.Cell --: --

  • DOI: 10.1016/j.molcel.2020.02.017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Transcription initiation requires formation of the open promoter complex (RPo). To generate RPo, RNA polymerase (RNAP) unwinds the DNA duplex to form the transcription bubble and loads the DNA into the RNAP active site. RPo formation is a multi-step ...

    Transcription initiation requires formation of the open promoter complex (RPo). To generate RPo, RNA polymerase (RNAP) unwinds the DNA duplex to form the transcription bubble and loads the DNA into the RNAP active site. RPo formation is a multi-step process with transient intermediates of unknown structure. We use single-particle cryoelectron microscopy to visualize seven intermediates containing Escherichia coli RNAP with the transcription factor TraR en route to forming RPo. The structures span the RPo formation pathway from initial recognition of the duplex promoter in a closed complex to the final RPo. The structures and supporting biochemical data define RNAP and promoter DNA conformational changes that delineate steps on the pathway, including previously undetected transient promoter-RNAP interactions that contribute to populating the intermediates but do not occur in RPo. Our work provides a structural basis for understanding RPo formation and its regulation, a major checkpoint in gene expression throughout evolution.


    Organizational Affiliation

    Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA. Electronic address: darst@rockefeller.edu.,Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.,Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein TraR
N
72Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: traR
Find proteins for P41065 (Escherichia coli (strain K12))
Go to UniProtKB:  P41065
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
G, H, M
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: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
I
1342Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
Find proteins for P0A8V4 (Escherichia coli O157:H7)
Go to UniProtKB:  P0A8V4
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
J
1430Escherichia 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: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
K
91Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for P0A802 (Escherichia coli O157:H7)
Go to UniProtKB:  P0A802
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor RpoD
L
616Escherichia coliMutation(s): 0 
Gene Names: rpoD
Find proteins for Q0P6L9 (Escherichia coli)
Go to UniProtKB:  Q0P6L9
Entity ID: 7
MoleculeChainsLengthOrganism
DNA (85-MER)O85Escherichia coli
Entity ID: 8
MoleculeChainsLengthOrganism
DNA (85-MER)P85Escherichia coli
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
J, N
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
1N7
Query on 1N7

Download SDF File 
Download CCD File 
I, J, L, N
CHAPSO
2-hydroxy-N,N-dimethyl-3-sulfo-N-(3-{[(3beta,5beta,7beta,12beta)-3,7,12-trihydroxy-24-oxocholan-24-yl]amino}propyl)propan-1-aminium
C32 H59 N2 O8 S
GUQQBLRVXOUDTN-XOHPMCGNSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United States--

Revision History 

  • Version 1.0: 2020-03-25
    Type: Initial release