4YLO

E. coli Transcription Initiation Complex - 16-bp spacer and 4-nt RNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.00 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.232 

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This is version 1.4 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: https://doi.org/10.1016/j.molcel.2015.03.010
  • Primary Citation of Related Structures:  
    4YLN, 4YLO, 4YLP

  • 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 processive RNA synthesis ...

    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.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha242Escherichia coliMutation(s): 0 
Gene Names: rpoA, EcE24377A_3778
EC: 2.7.7.6
UniProt
Find proteins for A7ZSI4 (Escherichia coli O139:H28 (strain E24377A / ETEC))
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UniProt GroupA7ZSI4
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC,
L [auth I],
U [auth O]		1,342Escherichia coliMutation(s): 0 
Gene Names: rpoB, EcE24377A_4528
EC: 2.7.7.6
UniProt
Find proteins for A7ZUK1 (Escherichia coli O139:H28 (strain E24377A / ETEC))
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UniProt GroupA7ZUK1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D,
M [auth J],
V [auth P]		1,407Escherichia coliMutation(s): 0 
Gene Names: rpoC, EcE24377A_4529
EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12))
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UniProt GroupP0A8T7
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE,
N [auth K],
W [auth Q]		90Escherichia coliMutation(s): 0 
Gene Names: rpoZ, EcE24377A_4152
EC: 2.7.7.6
UniProt
Find proteins for A7ZTK1 (Escherichia coli O139:H28 (strain E24377A / ETEC))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoDF,
O [auth L],
X [auth R]		628Escherichia coliMutation(s): 0 
Gene Names: rpoD, alt, b3067, JW3039
UniProt
Find proteins for P00579 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChainsLengthOrganismImage
NT strand DNA (49-MER)G [auth 1],
P [auth 4],
Y [auth 7]		49synthetic construct
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Entity ID: 7
MoleculeChainsLengthOrganismImage
T strand DNA (49-MER)H [auth 2],
Q [auth 5],
Z [auth 8]		49synthetic construct
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Entity ID: 8
MoleculeChainsLengthOrganismImage
RNA (5'-D(*(GTP))-R(P*AP*GP*U)-3')AA [auth 9],
I [auth 3],
R [auth 6]		4synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.00 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.232 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 240.888α = 90
b = 208.174β = 119.31
c = 256.323γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM057510

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-22
    Type: Initial release
  • Version 1.1: 2015-04-29
    Changes: Database references
  • Version 1.2: 2015-05-20
    Changes: Database references
  • Version 1.3: 2017-09-06
    Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence