7QH5 | pdb_00007qh5

The crystal structure of the sigma factor SigG1 from Streptomyces tsukubaensis NRRL18488


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.270 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7QH5

This is version 1.1 of the entry. See complete history

Literature

Crystal structures of Streptomyces tsukubaensis sigma factor SigG1 and anti-sigma RsfG.

Leite, J.P.Lourenco, F.Oliveira, R.Sousa, S.F.Mendes, M.V.Gales, L.

(2023) J Struct Biol 215: 108038-108038

  • DOI: https://doi.org/10.1016/j.jsb.2023.108038
  • Primary Citation Related Structures: 
    7QH3, 7QH5

  • PubMed Abstract: 

    Transcription of specific genes in bacteria under environmental stress is frequently initiated by extracytoplasmic function (ECF) σ factors. ECFs σ factors harbour two conserved domains, σ 2 and σ 4 , for transcription initiation by recognition of the promoter region and recruitment of RNA polymerase (RNAP). The crystal structure of Streptomyces tsukubaensis SigG1, an ECF56-family σ factor, was determined revealing σ 2 , σ 4 and the additional carboxi-terminal domain SnoaL_2 tightly packed in a compact conformation. The structure of anti-sigma RsfG was also determined by X-ray crystallography and shows a rare β-barrel fold. Analysis of the metal binding motifs inside the protein barrel are consistent with Fe(III) binding, which is in agreement with previous findings that the Streptomyces tsukubaensis ECF56 SigG1-RsfG system is involved in metal-ion homeostasis.


  • Organizational Affiliation
    • i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, Porto, Porto 4200-135, Portugal; IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, Porto, Porto 4200-135, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua Jorge de Viterbo Ferreira 228, Porto, Porto 4050-313, Portugal.

Macromolecule Content 

  • Total Structure Weight: 80.59 kDa 
  • Atom Count: 5,138 
  • Modeled Residue Count: 625 
  • Deposited Residue Count: 738 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA polymerase sigma factor
A, B
369Streptomyces tsukubensis NRRL18488Mutation(s): 0 
Gene Names: STSU_011570STSU_11560
UniProt
Find proteins for I2N5H1 (Streptomyces tsukubensis (strain DSM 42081 / NBRC 108919 / NRRL 18488 / 9993))
Explore I2N5H1 
Go to UniProtKB:  I2N5H1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI2N5H1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.270 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.639α = 90
b = 151.836β = 90
c = 128.18γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fundacao para a Ciencia e a TecnologiaPortugal--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-21
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Data collection, Database references