4YLN

E. coli Transcription Initiation Complex - 17-bp spacer and 4-nt RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.5 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structures of the E. coli Transcription Initiation Complexes with a Complete Bubble.

Zuo, Y.Steitz, T.A.

(2015) Mol.Cell 58: 534-540

  • DOI: 10.1016/j.molcel.2015.03.010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • During transcription initiation, RNA polymerase binds to promoter DNA to form an initiation complex containing a DNA bubble and enters into abortive cycles of RNA synthesis before escaping the promoter to transit into the elongation phase for process ...

    During transcription initiation, RNA polymerase binds to promoter DNA to form an initiation complex containing a DNA bubble and enters into abortive cycles of RNA synthesis before escaping the promoter to transit into the elongation phase for processive RNA synthesis. Here we present the crystal structures of E. coli transcription initiation complexes containing a complete transcription bubble and de novo synthesized RNA oligonucleotides at about 6-Å resolution. The structures show how RNA polymerase recognizes DNA promoters that contain spacers of different lengths and reveal a bridging interaction between the 5'-triphosphate of the nascent RNA and the σ factor that may function to stabilize the short RNA-DNA hybrids during the early stage of transcription initiation. The conformation of the RNA oligonucleotides and the paths of the DNA strands in the complete initiation complexes provide insights into the mechanism that controls both the abortive and productive RNA synthesis.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, New Haven, CT 06510, USA; Department of Chemistry, Yale University, New Haven, CT 06520, USA. Electronic address: thomas.steitz@yale.edu.,Department of Molecular Biophysics and Biochemistry, 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, G, H, M, N
242Escherichia coli O139:H28 (strain E24377A / ETEC)Mutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
Find proteins for A7ZSI4 (Escherichia coli O139:H28 (strain E24377A / ETEC))
Go to UniProtKB:  A7ZSI4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
C, I, O
1342Escherichia coli O139:H28 (strain E24377A / ETEC)Mutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
Find proteins for A7ZUK1 (Escherichia coli O139:H28 (strain E24377A / ETEC))
Go to UniProtKB:  A7ZUK1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
D, J, P
1407Escherichia coli O139:H28 (strain E24377A / ETEC)Mutation(s): 0 
Gene Names: rpoC
EC: 2.7.7.6
Find proteins for A7ZUK2 (Escherichia coli O139:H28 (strain E24377A / ETEC))
Go to UniProtKB:  A7ZUK2
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
E, K, Q
90Escherichia coli O139:H28 (strain E24377A / ETEC)Mutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for A7ZTK1 (Escherichia coli O139:H28 (strain E24377A / ETEC))
Go to UniProtKB:  A7ZTK1
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor RpoD
F, L, R
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
MoleculeChainsLengthOrganism
NT strand DNA (49-MER)1,4,749synthetic construct
Entity ID: 7
MoleculeChainsLengthOrganism
T strand DNA (49-MER)2,5,849synthetic construct
Entity ID: 8
MoleculeChainsLengthOrganism
RNA (5'-D(*(GTP))-R(P*AP*GP*U)-3')3,6,94synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
6, D, P
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GTP
Query on GTP
3, 6, 9
NON-POLYMERC10 H16 N5 O14 P3G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.5 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.245 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 237.401α = 90.00
b = 206.052β = 116.55
c = 248.690γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-03-05 
  • Released Date: 2015-04-22 
  • Deposition Author(s): Zuo, Y., Steitz, T.A.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM057510

Revision History 

  • Version 1.0: 2015-04-22
    Type: Initial release
  • Version 1.1: 2015-04-29
    Type: Database references
  • Version 1.2: 2015-05-20
    Type: Database references
  • Version 1.3: 2017-09-06
    Type: Advisory, Author supporting evidence, Database references, Derived calculations, Source and taxonomy