[English] 日本語
Yorodumi
- PDB-9j1l: Side fiber of monocin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9j1l
TitleSide fiber of monocin
Components
  • (FtbO) x 2
  • Alpha-amylase
  • FtbP
KeywordsVIRUS LIKE PARTICLE / Bacteriocin / bacteriophage / Siphoviridae / F-type tailocin / phage tail-like bacteriocins / Listeria monocytogenes / monocin / cryo-EM
Function / homology: / Alpha-amylase / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsWang, J.W. / Gu, Z.W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371254 China
National Natural Science Foundation of China (NSFC)32171190 China
CitationJournal: Nat Commun / Year: 2025
Title: Structure of an F-type phage tail-like bacteriocin from Listeria monocytogenes.
Authors: Zhiwei Gu / Xiaofei Ge / Jiawei Wang /
Abstract: F-type phage tail-like bacteriocins (PTLBs) are high-molecular-weight protein complexes exhibiting bactericidal activity and share evolutionary similarities with the tails of non-contractile ...F-type phage tail-like bacteriocins (PTLBs) are high-molecular-weight protein complexes exhibiting bactericidal activity and share evolutionary similarities with the tails of non-contractile siphoviruses. In this study, we present the atomic structure of monocin, a genetically engineered F-type PTLB from Listeria monocytogenes. Our detailed atomic-level analysis, excluding two chaperone proteins, provides crucial insights into the molecular architecture of F-type PTLBs. The core structure of monocin resembles TP901-1-like phage tails, featuring three side fibers with receptor-binding domains that connect to the baseplate for host adhesion. Based on these findings, we propose a potential mechanism by which F-type PTLBs induce cell death, offering a foundation for developing targeted antibacterial therapies.
History
DepositionAug 5, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release
Revision 1.0Jan 8, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 8, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 8, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 8, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 8, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 8, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.year / _em_admin.last_update
Revision 1.1Feb 26, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.year / _em_admin.last_update
Revision 1.2Mar 5, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.2Mar 5, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: Alpha-amylase
2: FtbP
3: FtbO
A: FtbP
B: FtbP
C: FtbP
I: FtbP
N: Alpha-amylase
O: FtbO
P: FtbP
Q: FtbP
R: FtbP
n: Alpha-amylase
o: FtbO
p: FtbP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)293,42217
Polymers293,31015
Non-polymers1122
Water00
1


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

-
Components

#1: Protein Alpha-amylase / FtbN


Mass: 21669.369 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria)
Gene: AF817_12260, AP104_04205, B4X68_12585, DG57_02060, EYJ21_12320, F1788_11040, FJL03_10560, GCV64_11985, GT011_12435, GYO01_10525, GYP27_04165, GYU24_12610, GZK27_10240
Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: A0A3D7WJE9
#2: Protein
FtbP


Mass: 19783.211 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria)
Gene: AF817_12270, AP104_04215, B4X68_12595, DG57_02070, EYJ21_12310, EZM42_13160, F1788_11050, FJL03_10570, FPL45_04495, GHO09_06960, GT011_12445, GYO01_10535, GYP27_04175, GYU24_12620, GZK27_10250
Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: A0A3R0H0Z2
#3: Protein FtbO


Mass: 17240.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria)
Gene: AP104_04210, B4X68_12590, EYJ21_12315, EZM42_13155, F1788_11045, FJL03_10565, FPL45_04490, GCV64_11990, GHO09_06955, GYO01_10530, GYP27_04170, GZK27_10245
Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: A0A3T2E047
#4: Protein FtbO


Mass: 15772.468 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria)
Gene: AP104_04210, B4X68_12590, EYJ21_12315, EZM42_13155, F1788_11045, FJL03_10565, FPL45_04490, GCV64_11990, GHO09_06955, GYO01_10530, GYP27_04170, GZK27_10245
Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: A0A3T2E047
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: monocin / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Listeria monocytogenes (bacteria)
Source (recombinant)Organism: Lactococcus lactis (lactic acid bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: PROPANE

-
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: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43630 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00820658
ELECTRON MICROSCOPYf_angle_d0.91227915
ELECTRON MICROSCOPYf_dihedral_angle_d4.2712751
ELECTRON MICROSCOPYf_chiral_restr0.0413132
ELECTRON MICROSCOPYf_plane_restr0.0033564

+
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