4OAY | pdb_00004oay

BldD CTD-c-di-GMP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.234 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4OAY

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

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 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.

Macromolecule Content 

  • Total Structure Weight: 139.8 kDa 
  • Atom Count: 8,828 
  • Modeled Residue Count: 928 
  • Deposited Residue Count: 1,092 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-binding protein91Streptomyces venezuelae ATCC 10712Mutation(s): 1 
Gene Names: SVEN_1089
UniProt
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
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C2E

Query on C2E



Download:Ideal Coordinates CCD File
AA [auth G]
BA [auth G]
CA [auth F]
DA [auth F]
EA [auth D]
AA [auth G],
BA [auth G],
CA [auth F],
DA [auth F],
EA [auth D],
FA [auth D],
GA [auth N],
HA [auth N],
IA [auth M],
JA [auth M],
M [auth A],
N [auth A],
O [auth B],
P [auth B],
Q [auth K],
R [auth K],
S [auth J],
T [auth J],
U [auth R],
V [auth R],
W [auth H],
X [auth H],
Y [auth E],
Z [auth E]
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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
B
C [auth K]
D [auth J]
E [auth R]
A,
B,
C [auth K],
D [auth J],
E [auth R],
F [auth H],
G [auth E],
H [auth G],
I [auth F],
J [auth D],
K [auth N],
L [auth M]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.234 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.5α = 90
b = 86.5β = 90
c = 151.48γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2015-09-16
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.3: 2024-10-16
    Changes: Structure summary