5IPL

SigmaS-transcription initiation complex with 4-nt nascent RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of E. coli sigma S-transcription initiation complexes provide new insights into polymerase mechanism.

Liu, B.Zuo, Y.Steitz, T.A.

(2016) Proc.Natl.Acad.Sci.USA 113: 4051-4056

  • DOI: 10.1073/pnas.1520555113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In bacteria, multiple σ factors compete to associate with the RNA polymerase (RNAP) core enzyme to form a holoenzyme that is required for promoter recognition. During transcription initiation RNAP remains associated with the upstream promoter DNA via ...

    In bacteria, multiple σ factors compete to associate with the RNA polymerase (RNAP) core enzyme to form a holoenzyme that is required for promoter recognition. During transcription initiation RNAP remains associated with the upstream promoter DNA via sequence-specific interactions between the σ factor and the promoter DNA while moving downstream for RNA synthesis. As RNA polymerase repetitively adds nucleotides to the 3'-end of the RNA, a pyrophosphate ion is generated after each nucleotide incorporation. It is currently unknown how the release of pyrophosphate affects transcription. Here we report the crystal structures of E coli transcription initiation complexes (TICs) containing the stress-responsive σ(S) factor, a de novo synthesized RNA oligonucleotide, and a complete transcription bubble (σ(S)-TIC) at about 3.9-Å resolution. The structures show the 3D topology of the σ(S) factor and how it recognizes the promoter DNA, including likely specific interactions with the template-strand residues of the -10 element. In addition, σ(S)-TIC structures display a highly stressed pretranslocated initiation complex that traps a pyrophosphate at the active site that remains closed. The position of the pyrophosphate and the unusual phosphodiester linkage between the two terminal RNA residues suggest an unfinished nucleotide-addition reaction that is likely at equilibrium between nucleotide addition and pyrophosphorolysis. Although these σ(S)-TIC crystals are enzymatically active, they are slow in nucleotide addition, as suggested by an NTP soaking experiment. Pyrophosphate release completes the nucleotide addition reaction and is associated with extensive conformational changes around the secondary channel but causes neither active site opening nor transcript translocation.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520; thomas.steitz@yale.edu yuhong.zuo@yale.edu.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520; Department of Chemistry, Yale University, New Haven, CT 06520 thomas.steitz@yale.edu yuhong.zuo@yale.edu.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520;




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
A, B
242Escherichia 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: 2
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: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
D
1407Escherichia 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: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
E
90Escherichia 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: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor RpoS
F
336Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoS (appR, katF, nur, otsX, sigS)
Find proteins for P13445 (Escherichia coli (strain K12))
Go to UniProtKB:  P13445
Entity ID: 6
MoleculeChainsLengthOrganism
synthetic nontemplate strand DNA (50-MER)150synthetic construct
Entity ID: 7
MoleculeChainsLengthOrganism
synthetic template strand DNA (50-MER)250synthetic construct
Entity ID: 8
MoleculeChainsLengthOrganism
nascent RNA 4-mer34synthetic construct
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
DPO
Query on DPO

Download SDF File 
Download CCD File 
C
DIPHOSPHATE
O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-J
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-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: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.247 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 131.710α = 90.00
b = 152.671β = 90.00
c = 226.698γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2016-04-13
    Type: Database references
  • Version 1.2: 2016-06-22
    Type: Database references