6N62

Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstream fork promoter DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.803 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.286 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structural mechanism of transcription inhibition by lasso peptides microcin J25 and capistruin.

Braffman, N.R., Piscotta, F.J., Hauver, J., Campbell, E.A., Link, A.J., Darst, S.A.

(2019) Proc. Natl. Acad. Sci. U.S.A. 116: 1273-1278


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
A, B
239Escherichia 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 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: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
D
1409Escherichia 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 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: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor RpoD
F
613Escherichia coliMutation(s): 0 
Gene Names: rpoD
Find proteins for Q0P6L9 (Escherichia coli)
Go to UniProtKB:  Q0P6L9
Entity ID: 6
MoleculeChainsLengthOrganism
non-template strand DNAN29Escherichia coli
Entity ID: 7
MoleculeChainsLengthOrganism
template strand DNAT24Escherichia coli
Small Molecules
Ligands 2 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.803 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.286 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 173.771α = 90.00
b = 173.771β = 90.00
c = 388.771γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR35 GM118130

Revision History 

  • Version 1.0: 2019-01-09
    Type: Initial release
  • Version 1.1: 2019-01-23
    Type: Data collection, Database references
  • Version 1.2: 2019-02-06
    Type: Data collection, Database references