› 4m1u

X-ray diffraction
1.56Å resolution

The crystal structure of Stx2 and a disaccharide ligand

Released:
DOI: 10.2210/pdb4m1u/pdb
PDB entry 4m1u coloured by chain, front view.
PDB entry 4m1u coloured by chain, side view.
PDB entry 4m1u coloured by chain, top view.
Source organisms:
Primary publication:
The crystal structure of shiga toxin type 2 with bound disaccharide guides the design of a heterobifunctional toxin inhibitor.
Jacobson JM, Yin J, Kitov PI, Mulvey G, Griener TP, James MN, Armstrong G, Bundle DR
J Biol Chem 289 885-94 (2014)
PMID: 24225957

Function and Biology Details

Reaction catalysed: 
Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-181498 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
rRNA N-glycosylase Chain: A
Molecule details ›
Chain: A
Length: 297 amino acids
Theoretical weight: 33.23 KDa
Source organism: Escherichia coli O157:H7
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7DI68 (Residues: 23-319; Coverage: 100%)
Gene names: ECs_1205, stx 2 A-subunit, stx2 A-subunit, stx2A
Sequence domains: Ribosome inactivating protein
Structure domains:
Stx2B Chains: B, C, D, E, F
Molecule details ›
Chains: B, C, D, E, F
Length: 70 amino acids
Theoretical weight: 7.82 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7DJJ2 (Residues: 20-89; Coverage: 100%)
Gene names: CLG78_003372, CLG78_005672, F7F11_25580, HI055_004506, HI055_004905, stx2B, stx2dB, stx2vB, stxB2, stxII, vtx2B
Sequence domains: Shiga-like toxin beta subunit
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)

Ligands and Environments

Carbohydrate polymer : NEW Components: MBG, A2G
Carbohydrate polymer
1 bound ligand:
Ligand 1PS 3 x 1PS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08B1-1
Spacegroup: P61
Unit cell:
a: 146.25Å b: 146.25Å c: 60.31Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.171 0.17 0.192
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Shiga Toxins as Multi-Functional Proteins: Induction of Host Cellular Stress Responses, Role in Pathogenesis and Therapeutic Applications.
Lee et al. (2016)
6 more

4 mentions without citation

Shiga Toxins: An Update on Host Factors and Biomedical Applications.
Liu et al. (2021)
3 more