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- EMDB-42963: CryoEM Structure of Diffocin - postcontracted - Baseplate - trans... -

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Basic information

Entry
Database: EMDB / ID: EMD-42963
TitleCryoEM Structure of Diffocin - postcontracted - Baseplate - transitional state
Map data
Sample
  • Complex: Diffocin
    • Protein or peptide: TRI-2 (CD1371)
    • Protein or peptide: Sheath (CD1363)
    • Protein or peptide: Sheath initiator (CD1370)
    • Protein or peptide: TRI-1 (CD1372)
KeywordsPhage tail-like / bacteriocin / baseplate / post-contraction / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


Bacteriophage Mu-like, Gp48 / : / Bacteriophage Mu-like, Gp48 / Protein of unknown function DUF2634 / Contractile injection system sheath initiator / Baseplate protein J-like / Baseplate J-like protein barrel domain / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.6 Å
AuthorsCai XY / He Y / Zhou ZH
Funding support United States, 3 items
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, 2023-
Header (metadata) releaseAug 28, 2024-
Map releaseAug 28, 2024-
UpdateAug 28, 2024-
Current statusAug 28, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42963.png

Downloads & links

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Map

FileDownload / File: emd_42963.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 300 pix.
= 330. Å		1.1 Å/pix.
x 300 pix.
= 330. Å		1.1 Å/pix.
x 300 pix.
= 330. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0141
Minimum - Maximum-0.026265675 - 0.043853536
Average (Standard dev.)0.00042939492 (±0.0044983244)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42963_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_42963_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_42963_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Diffocin

EntireName: Diffocin
Components
  • Complex: Diffocin
    • Protein or peptide: TRI-2 (CD1371)
    • Protein or peptide: Sheath (CD1363)
    • Protein or peptide: Sheath initiator (CD1370)
    • Protein or peptide: TRI-1 (CD1372)

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Supramolecule #1: Diffocin

SupramoleculeName: Diffocin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridioides difficile (bacteria)

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Macromolecule #1: TRI-2 (CD1371)

MacromoleculeName: TRI-2 (CD1371) / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria)
Molecular weightTheoretical: 39.603281 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString: MYSDQTYEVI KNRTLENINL DIYKGEGSFL NNMVSGNNLE LSKIYLELSK MHKMAFIQDT YNQFLDKRVN EFGVYRKLGT ESNGEVEFI GEKGTVINNG TIISYRDLLF VVIKDVTIGS EEGDNSPVQA LEVGKKYNLP TNCEFKLVDN ISGVTKITNT R SFEGGTDI ...String:
MYSDQTYEVI KNRTLENINL DIYKGEGSFL NNMVSGNNLE LSKIYLELSK MHKMAFIQDT YNQFLDKRVN EFGVYRKLGT ESNGEVEFI GEKGTVINNG TIISYRDLLF VVIKDVTIGS EEGDNSPVQA LEVGKKYNLP TNCEFKLVDN ISGVTKITNT R SFEGGTDI ETDEELKERF YKIQRNQATS GNKAHYEEWA LEVDGVYNVK VYPRWDGPGT VKVLIFGKNN QAVDTETIER CQ QHIDEEK PIGPTITVVT PLPIEISISA VMKLEDGYTL DNVKESFLES INTYFRDIRG EIIYTKVMGI LINTTGVHDL SNL LINGST DNITINEDKI PSVTTVNFSE VENQ

UniProtKB: Base plate protein

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Macromolecule #2: Sheath (CD1363)

MacromoleculeName: Sheath (CD1363) / type: protein_or_peptide / ID: 2 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria)
Molecular weightTheoretical: 39.26843 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString: MAIGLPSINI SFKELATTVK ERSARGIIAM VLKDAKALGL NEIHEKEDIP VDLSAENKEY INLALMGNVN TPNKLLVYVI EGEADIQTA LDFLETKEFN YLCMPKAVEA DKTAIKNWII KLRDIDKVKV KAVLGKVVGN HEGIINFTTE DVLVGEKKYS V DEFTSRVA ...String:
MAIGLPSINI SFKELATTVK ERSARGIIAM VLKDAKALGL NEIHEKEDIP VDLSAENKEY INLALMGNVN TPNKLLVYVI EGEADIQTA LDFLETKEFN YLCMPKAVEA DKTAIKNWII KLRDIDKVKV KAVLGKVVGN HEGIINFTTE DVLVGEKKYS V DEFTSRVA GLIAGTPLSQ SVTYTKLSDV VDIPKMTKVD AESRVNKGEL ILIKEAGAIR IARGVNSLTE LTAEKGEMFQ KI KIVDTLD IIHSDIRKVI IDDYIGKVTN SYDNKCLLIV AIKSYLEELE KSALIESDST VEIDFEAQKS YLKSKGVDLS YMT LQEIKE ANTGSKVFLK AKIKVLDAME DIDLSIEI

UniProtKB: Phage tail sheath protein

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Macromolecule #3: Sheath initiator (CD1370)

MacromoleculeName: Sheath initiator (CD1370) / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria)
Molecular weightTheoretical: 16.549959 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString:
MSTIFPFIGV PEDYILPKTE ELPIFREVAW DFEKDEPILE KGDFKIIEKK EALKVWIYKC IKTNRYEHEI YSLEYGTELS ELIGQKYTK GLTESEASRF IKEALLINPY ILEVNVKSAN FNRDILSANV KVSTIYGEVE INV

UniProtKB: DUF2634 domain-containing protein

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Macromolecule #4: TRI-1 (CD1372)

MacromoleculeName: TRI-1 (CD1372) / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria)
Molecular weightTheoretical: 26.473488 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString: MKLIDKLPSF DRNYIVEEIQ GAYDTELNIL KEDIDDTFNQ LFVDTATWGL DMWEDILCIE KKELDFDTRR SNIKAKMRSR GTSTIEVIK SICEAYTKSE TDIKVYSDEF TFVLSFIANN CDYKTLLDCS DMIERVKPAH LLHYLEPIIL DKSMVYCGGG M VCSEEVKV ...String:
MKLIDKLPSF DRNYIVEEIQ GAYDTELNIL KEDIDDTFNQ LFVDTATWGL DMWEDILCIE KKELDFDTRR SNIKAKMRSR GTSTIEVIK SICEAYTKSE TDIKVYSDEF TFVLSFIANN CDYKTLLDCS DMIERVKPAH LLHYLEPIIL DKSMVYCGGG M VCSEEVKV HPYFEPIIKC SAVVNCGAGM ISREEIKVYP LSIKCIENNC KINIAIANDT GVENVVVYPK SEVV

UniProtKB: Base plate protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11345
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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