5VL9

Crystal structure of EilR in complex with eilO DNA element


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Jungle Express is a versatile repressor system for tight transcriptional control.

Ruegg, T.L.Pereira, J.H.Chen, J.C.DeGiovanni, A.Novichkov, P.Mutalik, V.K.Tomaleri, G.P.Singer, S.W.Hillson, N.J.Simmons, B.A.Adams, P.D.Thelen, M.P.

(2018) Nat Commun 9: 3617-3617

  • DOI: https://doi.org/10.1038/s41467-018-05857-3
  • Primary Citation of Related Structures:  
    5VL9, 5VLG, 5VLM

  • PubMed Abstract: 

    Tightly regulated promoters are essential for numerous biological applications, where strong inducibility, portability, and scalability are desirable. Current systems are often incompatible with large-scale fermentations due to high inducer costs and strict media requirements. Here, we describe the bottom-up engineering of 'Jungle Express', an expression system that enables efficient gene regulation in diverse proteobacteria. This system is guided by EilR, a multidrug-binding repressor with high affinity to its optimized operator and cationic dyes that act as powerful inducers at negligible costs. In E. coli, the engineered promoters exhibit minimal basal transcription and are inducible over four orders of magnitude by 1 µM crystal violet, reaching expression levels exceeding those of the strongest current bacterial systems. Further, we provide molecular insights into specific interactions of EilR with its operator and with two inducers. The versatility of Jungle Express opens the way for tightly controlled and efficient gene expression that is not restricted to host organism, substrate, or scale.


  • Organizational Affiliation

    Joint BioEnergy Institute, Emeryville, CA, 94608, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Regulatory protein TetR
A, B, C, D
192[Enterobacter] lignolyticusMutation(s): 0 
Gene Names: Entcl_2353
UniProt
Find proteins for E3G817 (Enterobacter lignolyticus (strain SCF1))
Explore E3G817 
Go to UniProtKB:  E3G817
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE3G817
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*AP*TP*GP*TP*CP*CP*AP*AP*CP*TP*TP*TP*C)-3')
E, G
14[Enterobacter] lignolyticus
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*AP*AP*AP*GP*TP*TP*GP*GP*AP*CP*AP*TP*A)-3')
F, H
14[Enterobacter] lignolyticus
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEZ
Query on HEZ

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth B]
L [auth B]
M [auth B]
I [auth A],
J [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth C],
O [auth D],
P [auth D],
Q [auth D]
HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.79α = 116.8
b = 74.06β = 105.19
c = 81.36γ = 90.78
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-AC02-05CH11231

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2018-11-28
    Changes: Data collection, Database references
  • Version 1.2: 2020-02-26
    Changes: Derived calculations
  • Version 1.3: 2022-03-16
    Changes: Author supporting evidence, Database references