6QFD

The complex structure of hsRosR-S4 (vng0258/RosR-S4)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


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


Literature

Specificity of protein-DNA interactions in hypersaline environment: structural studies on complexes of Halobacterium salinarum oxidative stress-dependent protein hsRosR.

Kutnowski, N., Shmulevich, F., Davidov, G., Shahar, A., Bar-Zvi, D., Eichler, J., Zarivach, R., Shaanan, B.

(2019) Nucleic Acids Res 47: 8860-8873

  • DOI: https://doi.org/10.1093/nar/gkz604
  • Primary Citation of Related Structures:  
    6QFD, 6QH0, 6QIL, 6QUA

  • PubMed Abstract: 

    • Interactions between proteins and DNA are crucial for all biological systems. Many studies have shown the dependence of protein-DNA interactions on the surrounding salt concentration. How these interactions are maintained in the hypersaline environments that halophiles inhabit remains puzzling ...

    Interactions between proteins and DNA are crucial for all biological systems. Many studies have shown the dependence of protein-DNA interactions on the surrounding salt concentration. How these interactions are maintained in the hypersaline environments that halophiles inhabit remains puzzling. Towards solving this enigma, we identified the DNA motif recognized by the Halobactrium salinarum ROS-dependent transcription factor (hsRosR), determined the structure of several hsRosR-DNA complexes and investigated the DNA-binding process under extreme high-salt conditions. The picture that emerges from this work contributes to our understanding of the principles underlying the interplay between electrostatic interactions and salt-mediated protein-DNA interactions in an ionic environment characterized by molar salt concentrations.

    Organizational Affiliation: 

    Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410510, Israel.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-binding protein
A, B, C, D
116Halobacterium salinarum NRC-1Mutation(s): 0 
Gene Names: VNG_0258H, rosR
UniProt
Find proteins for Q9HSF4 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Explore Q9HSF4 
Go to UniProtKB:  Q9HSF4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HSF4
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (28-MER)
E, G
28Halobacterium salinarum NRC-1
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (28-MER)
F, H
28Halobacterium salinarum NRC-1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
EA [auth D]
FA [auth D]
GA [auth D]
AA [auth C],
BA [auth C],
EA [auth D],
FA [auth D],
GA [auth D],
HA [auth D],
I [auth A],
IA [auth D],
J [auth A],
K [auth A],
KA [auth E],
L [auth A],
LA [auth E],
M [auth A],
MA [auth F],
N [auth A],
NA [auth G],
OA [auth G],
PA [auth H],
Q [auth B],
QA [auth H],
R [auth B],
S [auth B],
T [auth B],
X [auth C],
Y [auth C],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
MN
Query on MN
Download Ideal Coordinates CCD File 
CA [auth C]
DA [auth C]
JA [auth D]
O [auth A]
P [auth A]
CA [auth C],
DA [auth C],
JA [auth D],
O [auth A],
P [auth A],
U [auth B],
V [auth B],
W [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.805α = 81.53
b = 83.995β = 86.18
c = 88.876γ = 74.48
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael1382/13

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2019-07-24
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-23
    Changes: Data collection, Database references