6PFJ

Structure of S. venezuelae RsiG-WhiG-(ci-di-GMP) complex, P64 crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

c-di-GMP Arms an Anti-sigma to Control Progression of Multicellular Differentiation in Streptomyces.

Gallagher, K.A.Schumacher, M.A.Bush, M.J.Bibb, M.J.Chandra, G.Holmes, N.A.Zeng, W.Henderson, M.Zhang, H.Findlay, K.C.Brennan, R.G.Buttner, M.J.

(2020) Mol Cell 77: 586

  • DOI: https://doi.org/10.1016/j.molcel.2019.11.006
  • Primary Citation of Related Structures:  
    6PFJ, 6PFV

  • PubMed Abstract: 

    Streptomyces are our primary source of antibiotics, produced concomitantly with the transition from vegetative growth to sporulation in a complex developmental life cycle. We previously showed that the signaling molecule c-di-GMP binds BldD, a master repressor, to control initiation of development. Here we demonstrate that c-di-GMP also intervenes later in development to control differentiation of the reproductive hyphae into spores by arming a novel anti-σ (RsiG) to bind and sequester a sporulation-specific σ factor (σ WhiG ). We present the structure of the RsiG-(c-di-GMP) 2 WhiG complex, revealing an unusual, partially intercalated c-di-GMP dimer bound at the RsiG-σ WhiG interface. RsiG binds c-di-GMP in the absence of σ WhiG , employing a novel E(X) 3 S(X) 2 R(X) 3 Q(X) 3 D motif repeated on each helix of a coiled coil. Further studies demonstrate that c-di-GMP is essential for RsiG to inhibit σ WhiG . These findings reveal a newly described control mechanism for σ-anti-σ complex formation and establish c-di-GMP as the central integrator of Streptomyces development.


  • Organizational Affiliation

    Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AmfC proteinA [auth T]176Streptomyces venezuelae ATCC 10712Mutation(s): 1 
Gene Names: SVEN_3933
UniProt
Find proteins for F2RFR7 (Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745))
Explore F2RFR7 
Go to UniProtKB:  F2RFR7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2RFR7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase sigma factorB [auth A]278Streptomyces sp. PanSC19Mutation(s): 4 
Gene Names: EDD98_3685
UniProt
Find proteins for A0A3N1Q704 (Streptomyces sp. PanSC19)
Explore A0A3N1Q704 
Go to UniProtKB:  A0A3N1Q704
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3N1Q704
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C2E
Query on C2E

Download Ideal Coordinates CCD File 
C [auth T],
D [auth T]
9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
C20 H24 N10 O14 P2
PKFDLKSEZWEFGL-MHARETSRSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
C2E Binding MOAD:  6PFJ Kd: 390 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.089α = 90
b = 92.089β = 90
c = 96.646γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
AutoSolphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references
  • Version 1.2: 2020-02-19
    Changes: Database references, Structure summary
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references