6B6H

The cryo-EM structure of a bacterial class I transcription activation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis of bacterial transcription activation.

Liu, B.Hong, C.Huang, R.K.Yu, Z.Steitz, T.A.

(2017) Science 358: 947-951

  • DOI: 10.1126/science.aao1923

  • PubMed Abstract: 
  • In bacteria, the activation of gene transcription at many promoters is simple and only involves a single activator. The cyclic adenosine 3',5'-monophosphate receptor protein (CAP), a classic activator, is able to activate transcription independently ...

    In bacteria, the activation of gene transcription at many promoters is simple and only involves a single activator. The cyclic adenosine 3',5'-monophosphate receptor protein (CAP), a classic activator, is able to activate transcription independently through two different mechanisms. Understanding the class I mechanism requires an intact transcription activation complex (TAC) structure at a high resolution. Here we report a high-resolution cryo-electron microscopy structure of an intact Escherichia coli class I TAC containing a CAP dimer, a σ 70 -RNA polymerase (RNAP) holoenzyme, a complete class I CAP-dependent promoter DNA, and a de novo synthesized RNA oligonucleotide. The structure shows how CAP wraps the upstream DNA and how the interactions recruit RNAP. Our study provides a structural basis for understanding how activators activate transcription through the class I recruitment mechanism.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. thomas.steitz@yale.edu yuz@janelia.hhmi.org.,Howard Hughes Medical Institute, CryoEM Shared Resource, Janelia Research Campus, Ashburn, VA 20147, USA.,Howard Hughes Medical Institute, CryoEM Shared Resource, Janelia Research Campus, Ashburn, VA 20147, USA. thomas.steitz@yale.edu yuz@janelia.hhmi.org.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT 06510, USA.,Department of Chemistry, Yale University, New Haven, CT 06520, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
A, B
329Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
Find proteins for P0A7Z6 (Escherichia coli O157:H7)
Go to UniProtKB:  P0A7Z6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
C
1342Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
Find proteins for B7MIX3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MIX3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
D
1407Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoC
EC: 2.7.7.6
Find proteins for P0A8T8 (Escherichia coli O157:H7)
Go to UniProtKB:  P0A8T8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
E
91Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for B7MFL0 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MFL0
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor RpoD
F
628Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoD (alt)
Find proteins for P00579 (Escherichia coli (strain K12))
Go to UniProtKB:  P00579
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
cAMP-activated global transcriptional regulator CRP
G, H
210Escherichia coli O157:H7Mutation(s): 0 
Gene Names: crp
Find proteins for P0ACK0 (Escherichia coli O157:H7)
Go to UniProtKB:  P0ACK0
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
I
75Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
Find proteins for P0A7Z6 (Escherichia coli O157:H7)
Go to UniProtKB:  P0A7Z6
Entity ID: 8
MoleculeChainsLengthOrganism
SYNTHETIC NONTEMPLATE STRAND DNA (88-MER)188Escherichia coli
Entity ID: 9
MoleculeChainsLengthOrganism
SYNTHETIC TEMPLATE STRAND DNA (88-MER)288Escherichia coli
Entity ID: 10
MoleculeChainsLengthOrganism
NASCENT RNA 3-MER33Escherichia coli
Small Molecules
Ligands 3 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
CMP
Query on CMP

Download SDF File 
Download CCD File 
G, H
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
CYCLIC AMP; CAMP
C10 H12 N5 O6 P
IVOMOUWHDPKRLL-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GTP
Query on GTP
3
NON-POLYMERC10 H16 N5 O14 P3G
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 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 Institute of General Medical SciencesUnited StatesGM22778

Revision History 

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2017-11-29
    Type: Database references
  • Version 1.2: 2017-12-06
    Type: Author supporting evidence
  • Version 1.3: 2018-07-18
    Type: Data collection