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- PDB-8v43: CryoEM Structure of Diffocin - postcontracted - Baseplate - final... -

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Basic information

Entry
Database: PDB / ID: 8v43
TitleCryoEM Structure of Diffocin - postcontracted - Baseplate - final state
Components
  • Sheath (CD1363)
  • Sheath initiator (CD1370)
  • TRI-1 (CD1372)
  • TRI-2 (CD1371)
KeywordsVIRUS LIKE PARTICLE / Phage tail-like / bacteriocin / baseplate / post-contraction
Function / homology
Function and homology information


Bacteriophage Mu-like, Gp48 / Protein of unknown function DUF2634 / Bacteriophage Mu-like, Gp48 / Protein of unknown function (DUF2634) / : / Baseplate protein J-like / Baseplate J-like protein / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain
Similarity search - Domain/homology
DUF2634 domain-containing protein / Base plate protein / Base plate protein / Phage tail sheath protein
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsCai, X.Y. / He, Y. / Zhou, Z.H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI085318 United States
CitationJournal: Nat Commun / Year: 2024
Title: Atomic structures of a bacteriocin targeting Gram-positive bacteria.
Authors: Xiaoying Cai / Yao He / Iris Yu / Anthony Imani / Dean Scholl / Jeff F Miller / Z Hong Zhou /
Abstract: Due to envelope differences between Gram-positive and Gram-negative bacteria, engineering precision bactericidal contractile nanomachines requires atomic-level understanding of their structures; ...Due to envelope differences between Gram-positive and Gram-negative bacteria, engineering precision bactericidal contractile nanomachines requires atomic-level understanding of their structures; however, only those killing Gram-negative bacteria are currently known. Here, we report the atomic structures of an engineered diffocin, a contractile syringe-like molecular machine that kills the Gram-positive bacterium Clostridioides difficile. Captured in one pre-contraction and two post-contraction states, each structure fashions six proteins in the bacteria-targeting baseplate, two proteins in the energy-storing trunk, and a collar linking the sheath with the membrane-penetrating tube. Compared to contractile machines targeting Gram-negative bacteria, major differences reside in the baseplate and contraction magnitude, consistent with target envelope differences. The multifunctional hub-hydrolase protein connects the tube and baseplate and is positioned to degrade peptidoglycan during penetration. The full-length tape measure protein forms a coiled-coil helix bundle homotrimer spanning the entire diffocin. Our study offers mechanical insights and principles for designing potent protein-based precision antibiotics.
History
DepositionNov 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
v: TRI-2 (CD1371)
A: TRI-1 (CD1372)
j: Sheath initiator (CD1370)
P: Sheath (CD1363)
C: Sheath (CD1363)
D: Sheath (CD1363)
B: TRI-2 (CD1371)
m: TRI-2 (CD1371)
L: TRI-1 (CD1372)
i: Sheath initiator (CD1370)
f: Sheath (CD1363)
S: Sheath (CD1363)
V: Sheath (CD1363)
O: TRI-2 (CD1371)
n: TRI-2 (CD1371)
M: TRI-1 (CD1372)
k: Sheath initiator (CD1370)
g: Sheath (CD1363)
T: Sheath (CD1363)
W: Sheath (CD1363)
Q: TRI-2 (CD1371)
K: TRI-2 (CD1371)
E: TRI-1 (CD1372)
J: Sheath initiator (CD1370)
I: Sheath (CD1363)
G: Sheath (CD1363)
H: Sheath (CD1363)
F: TRI-2 (CD1371)
o: TRI-2 (CD1371)
N: TRI-1 (CD1372)
l: Sheath initiator (CD1370)
h: Sheath (CD1363)
U: Sheath (CD1363)
X: Sheath (CD1363)
R: TRI-2 (CD1371)
e: TRI-2 (CD1371)
Y: TRI-1 (CD1372)
d: Sheath initiator (CD1370)
c: Sheath (CD1363)
a: Sheath (CD1363)
b: Sheath (CD1363)
Z: TRI-2 (CD1371)


Theoretical massNumber of molelcules
Total (without water)1,440,21242
Polymers1,440,21242
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
TRI-2 (CD1371)


Mass: 39603.281 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: rtbJ / Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A1X9JZB1
#2: Protein
TRI-1 (CD1372)


Mass: 26473.488 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: rtbK / Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A1X9JZH3
#3: Protein
Sheath initiator (CD1370)


Mass: 16549.959 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: BN1095_340097 / Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A069AE46
#4: Protein
Sheath (CD1363)


Mass: 39268.430 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: SAMEA3375112_00264 / Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A9Q7ZU73

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Diffocin / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Clostridioides difficile (bacteria)
Source (recombinant)Organism: Bacillus subtilis (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11219 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00296612
ELECTRON MICROSCOPYf_angle_d0.451130452
ELECTRON MICROSCOPYf_dihedral_angle_d3.85912798
ELECTRON MICROSCOPYf_chiral_restr0.04115486
ELECTRON MICROSCOPYf_plane_restr0.00316506

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