Structure of 1.75 A BldD C-domain-c-di-GMP complex

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 

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Tetrameric c-di-GMP mediates effective transcription factor dimerization to control Streptomyces development.

Tschowri, N.Schumacher, M.A.Schlimpert, S.Chinnam, N.B.Findlay, K.C.Brennan, R.G.Buttner, M.J.

(2014) Cell 158: 1136-1147

  • DOI: https://doi.org/10.1016/j.cell.2014.07.022
  • Primary Citation of Related Structures:  
    4OAY, 4OAZ, 4OB4, 5KHD

  • PubMed Abstract: 

    The cyclic dinucleotide c-di-GMP is a signaling molecule with diverse functions in cellular physiology. Here, we report that c-di-GMP can assemble into a tetramer that mediates the effective dimerization of a transcription factor, BldD, which controls the progression of multicellular differentiation in sporulating actinomycete bacteria. BldD represses expression of sporulation genes during vegetative growth in a manner that depends on c-di-GMP-mediated dimerization. Structural and biochemical analyses show that tetrameric c-di-GMP links two subunits of BldD through their C-terminal domains, which are otherwise separated by ~10 Å and thus cannot effect dimerization directly. Binding of the c-di-GMP tetramer by BldD is selective and requires a bipartite RXD-X8-RXXD signature. The findings indicate a unique mechanism of protein dimerization and the ability of nucleotide signaling molecules to assume alternative oligomeric states to effect different functions.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-binding proteinA [auth R],
B [auth A]
91Streptomyces venezuelae ATCC 10712Mutation(s): 0 
Gene Names: SVEN_1089
Find proteins for F2RCL8 (Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745))
Explore F2RCL8 
Go to UniProtKB:  F2RCL8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2RCL8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on C2E

Download Ideal Coordinates CCD File 
C [auth R],
D [auth R],
E [auth A],
F [auth A]
C20 H24 N10 O14 P2
Binding Affinity Annotations 
IDSourceBinding Affinity
C2E Binding MOAD:  5KHD Kd: 2500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.16α = 90
b = 95.58β = 90
c = 99.58γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Structure summary