9OEE | pdb_00009oee

S. griseus TUA bound UmbA4 complexes


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The unique architecture of umbrella toxins permits a two-tiered molecular bet-hedging strategy for interbacterial antagonism.

Zhao, Q.Vlach, J.Park, Y.J.Tan, Y.Bertolli, S.K.Srinivas, P.Liao, P.Fitzpatrick, C.R.Dangl, J.L.Azadi, P.DiMaio, F.Peterson, S.B.Zhang, D.Veesler, D.Mougous, J.D.

(2025) Cell 

  • DOI: https://doi.org/10.1016/j.cell.2025.10.044
  • Primary Citation of Related Structures:  
    9OEE

  • PubMed Abstract: 

    Bacteria exist in competitive and rapidly changing environments in which the nature of future threats cannot be easily predicted. Streptomyces coelicolor produces three antibacterial umbrella particles that harbor distinct polymorphic toxin domains and an overlapping set of six diversified lectins. Here, we show that the exquisite specificity of umbrella particles derives from lectin-mediated species-specific binding to previously undescribed hypervariable surface glycoconjugates. A cryo-electron microscopy (cryo-EM) structure of one such lectin in complex with its oligosaccharide substrate defines the molecular basis for targeting through the coordinated recognition of multiple glycan features. Biochemical and genetic studies of several target species, in conjunction with lectin-swapping experiments, support a model whereby S. coelicolor umbrella toxin diversification at the levels of lectin composition and toxin polymorphism represents a unique, two-tiered bet-hedging strategy. Bioinformatic analyses support this as a means by which the unusual architecture of umbrella toxins offers Streptomyces a generalizable strategy to antagonize an unpredictable array of competitors.


  • Organizational Affiliation
    • Department of Microbiology, University of Washington, Seattle, WA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Secreted esteraseA,
B,
C [auth D],
D [auth F],
E [auth H]
696Streptomyces coelicolorMutation(s): 0 
UniProt
Find proteins for Q93J50 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q93J50 
Go to UniProtKB:  Q93J50
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93J50
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CAZ
Query on A1CAZ

Download Ideal Coordinates CCD File 
EB [auth H],
FA [auth D],
MB [auth H],
Q [auth A],
T [auth B]
2,3-diacetamido-4-O-acetyl-2,3-dideoxy-beta-D-mannopyranuronic acid
C12 H18 N2 O8
HTLNSXWBVAGZRH-UWKFXHKCSA-N
A1CAY
Query on A1CAY

Download Ideal Coordinates CCD File 
AB [auth F]
BA [auth B]
BB [auth F]
CA [auth B]
DB [auth H]
AB [auth F],
BA [auth B],
BB [auth F],
CA [auth B],
DB [auth H],
EA [auth D],
I [auth A],
J [auth A],
JA [auth D],
JB [auth H],
KA [auth D],
KB [auth H],
LB [auth H],
M [auth A],
N [auth A],
NA [auth D],
OA [auth D],
P [auth A],
RA [auth F],
S [auth B],
SA [auth F],
X [auth B],
Y [auth B],
YA [auth F],
ZA [auth F]
2,3-diacetamido-2,3-dideoxy-beta-D-mannopyranuronic acid
C10 H16 N2 O7
SOXOUCOZZYMXPU-XPMMEUEASA-N
A2G
Query on A2G

Download Ideal Coordinates CCD File 
AA [auth B]
CB [auth H]
DA [auth D]
F [auth A]
FB [auth H]
AA [auth B],
CB [auth H],
DA [auth D],
F [auth A],
FB [auth H],
G [auth A],
GA [auth D],
GB [auth H],
H [auth A],
HA [auth D],
HB [auth H],
IA [auth D],
IB [auth H],
K [auth A],
L [auth A],
LA [auth D],
MA [auth D],
O [auth A],
PA [auth F],
QA [auth F],
R [auth B],
TA [auth F],
U [auth B],
UA [auth F],
V [auth B],
VA [auth F],
W [auth B],
WA [auth F],
XA [auth F],
Z [auth B]
2-acetamido-2-deoxy-alpha-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States75N93022C00036

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release