BMRB Entry 17784

Title:
NMR structure of the PhyRSL-NepR complex from Sphingomonas sp. Fr1
Deposition date:
2011-07-18
Original release date:
2012-04-18
Authors:
Campagne, Sebastien; Damberger, Fred; Vorholt, Julia; Allain, Frederic
Citation:

Citation: Campagne, Sebastien; Damberger, Fred; Kaczmarczyk, Andreas; Francez-Charlot, Anne; Allain, Frederic H-T; Vorholt, Julia. "Structural basis for sigma factor mimicry in the general stress response of Alphaproteobacteria."  Proc. Natl. Acad. Sci. U.S.A. 109, E1405-E1414 (2012).
PubMed: 22550171

Assembly members:

Assembly members:
PhyR_sigma_like_domain, polymer, 157 residues, 17336.539 Da.
NepR_anti_sigma_factor, polymer, 62 residues, 6923.098 Da.

Natural source:

Natural source:   Common Name: Sphingomonas sp. Fr1   Taxonomy ID: 907061   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Sphingomonas Sphingomonas sp. Fr1

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET26bII-PhyRSL

Data sets:
Data typeCount
13C chemical shifts831
15N chemical shifts212
1H chemical shifts1415

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1PhyR_sigma_like_domain1
2NepR_anti_sigma_factor2

Entities:

Entity 1, PhyR_sigma_like_domain 157 residues - 17336.539 Da.

From residue 144 to 157, amino acid residues of thrombin cleavage site + his tag

1   METSERLEUGLYGLNGLNLEUALAPROHIS
2   LEUPROPHELEUARGARGTYRGLYARGALA
3   LEUTHRGLYSERGLNASNGLNGLYASPLYS
4   TYRVALARGALATHRLEUGLUALAILEVAL
5   ALAALAPROASPGLNPHEPROARGASPVAL
6   ASPPROARGLEUGLYLEUTYRARGMETPHE
7   GLNGLYILETRPALASERALAASNALAASP
8   GLYGLUALAGLNTHRSERGLNSERASPALA
9   GLUGLYTHRGLUALAVALALAARGALAARG
10   LEUALAARGMETTHRPROLEUSERARGGLN
11   ALALEULEULEUTHRALAMETGLUGLYPHE
12   SERPROGLUASPALAALATYRLEUILEGLU
13   VALASPTHRSERGLUVALGLUTHRLEUVAL
14   THRGLUALALEUALAGLUILEGLULYSGLN
15   THRARGALALEUGLULEUVALPROARGGLY
16   SERHISHISHISHISHISHIS

Entity 2, NepR_anti_sigma_factor 62 residues - 6923.098 Da.

1   METLEUASPLEUPROGLYASNLYSASPLYS
2   LYSALASERSERLYSLYSSERPROALALYS
3   VALGLNSERLYSASPARGASPMETGLYALA
4   ALALEUARGSERALATYRGLNLYSTHRILE
5   GLUGLUGLNVALPROASPGLUMETLEUASP
6   LEULEUASNLYSLEUALALEUGLULEUVAL
7   PROARG

Samples:

sample_1: PhyR sigma like domain, [U-100% 13C; U-100% 15N], 0.8 ± 0.02 mM; NepR anti sigma factor 0.8 ± 0.02 mM; sodium chloride 50 ± 0.05 mM; sodium phosphate 10 ± 0.01 mM; H2O 90%; D2O 10%

sample_2: PhyR sigma like domain 0.8 ± 0.02 mM; NepR anti sigma factor, [U-100% 13C; U-100% 15N], 0.8 ± 0.02 mM; sodium chloride 50 ± 0.05 mM; sodium phosphate 10 ± 0.01 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.06 M; pH: 6.8; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_1

Software:

CARA, Keller and Wuthrich - chemical shift assignment

UNIO v10, (Torsten Herrmann) - peak picking

CYANA v3, CYANA (Peter Guntert) - structure solution

AMBER v8, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

TOPSPIN v2.1, Bruker Biospin - processing

Molmol v2.2K, Koradi, Billeter and Wuthrich - data analysis

PyMol v1.3, Schrodinger, LLC. - data analysis

NMR spectrometers:

  • Bruker Avance 500 MHz
  • Bruker Avance 600 MHz
  • Bruker Avance 700 MHz
  • Bruker Avance 900 MHz

Related Database Links:

PDB
GB AET62591 KIU26946 AET62590
REF WP_017979560 WP_043060725

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks