[English] 日本語
Yorodumi
- EMDB-42962: CryoEM Structure of Diffocin - postcontracted - Collar - final state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-42962
TitleCryoEM Structure of Diffocin - postcontracted - Collar - final state
Map data
Sample
  • Complex: Diffocin
    • Protein or peptide: Tube (CD1364)
    • Protein or peptide: Sheath (CD1363)
    • Protein or peptide: Collar (CD1362)
KeywordsPhage tail-like / bacteriocin / collar / post-contraction / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


: / Domain of unknown function (DUF6838) / Phage tail tube protein / XkdM-like superfamily / Phage tail tube 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
Phage portal protein / RtbA / Phage tail sheath protein
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 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

-
Structure visualization

Supplemental images

emd_42962.png

Downloads & links

-
Map

FileDownload / File: emd_42962.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: 0.026
Minimum - Maximum-0.05282455 - 0.11466713
Average (Standard dev.)0.00086019025 (±0.007372404)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_42962_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_42962_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_42962_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Diffocin

EntireName: Diffocin
Components
  • Complex: Diffocin
    • Protein or peptide: Tube (CD1364)
    • Protein or peptide: Sheath (CD1363)
    • Protein or peptide: Collar (CD1362)

-
Supramolecule #1: Diffocin

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

-
Macromolecule #1: Tube (CD1364)

MacromoleculeName: Tube (CD1364) / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria)
Molecular weightTheoretical: 16.028353 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString:
MANMEARNVM SGTWGELWLD GNKVAEVKKF QAKMEFTKED IIIAGQMGTD TKYMGYKGKG SITLYHVSSR MHKLIGEKIK RGSEPRFVA ISKLNDPDSY GAERIAVKNI AFDDLTLADW EVGVKGEIEA PFTFTEYDFL DII

UniProtKB: Phage portal protein

-
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

-
Macromolecule #3: Collar (CD1362)

MacromoleculeName: Collar (CD1362) / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria)
Molecular weightTheoretical: 17.198816 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString:
MLKYKEILET IIEILKKNFT ESIFIDDESV QGSEGSCFFV SILSVICTPV MLNTNNKDIV ISIKYLPKPQ SKSIRMYEIS DELNKLFNR NIKVTDRKLN ITKLEQSIKK EESIYVLNFT FTLNYLDSVY EEDVVYENMK EINLNLGE

UniProtKB: RtbA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12152
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more