[English] 日本語
Yorodumi
- EMDB-46576: Structure of Citrobacter multi-ubiquitin protein filament -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-46576
TitleStructure of Citrobacter multi-ubiquitin protein filament
Map data
Sample
  • Complex: Filament assembly of Citrobacter sp. ubiquitin-like (Ubl) protein with Ca ion
    • Protein or peptide: Multi-ubiquitin domain-containing protein
  • Ligand: CALCIUM ION
Keywordsfilament / beta-grasp / PROTEIN BINDING
Biological speciesCitrobacter sp. RHBSTW-00271 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.43 Å
AuthorsGong M / Gu Y / Corbett KD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM144121 United States
CitationJournal: Structure / Year: 2025
Title: Structural diversity and oligomerization of bacterial ubiquitin-like proteins.
Authors: Minheng Gong / Qiaozhen Ye / Yajie Gu / Lydia R Chambers / Andrey A Bobkov / Neal K Arakawa / Mariusz Matyszewski / Kevin D Corbett /
Abstract: Bacteria possess a variety of operons with homology to eukaryotic ubiquitination pathways that encode predicted E1, E2, E3, deubiquitinase, and ubiquitin-like proteins. Some of these pathways have ...Bacteria possess a variety of operons with homology to eukaryotic ubiquitination pathways that encode predicted E1, E2, E3, deubiquitinase, and ubiquitin-like proteins. Some of these pathways have recently been shown to function in anti-bacteriophage immunity, but the biological functions of others remain unknown. Here, we show that ubiquitin-like proteins in two bacterial operon families show surprising architectural diversity, possessing one to three β-grasp domains preceded by diverse N-terminal domains. We find that a large group of bacterial ubiquitin-like proteins possess three β-grasp domains and form homodimers and helical filaments mediated by conserved Ca ion binding sites. Our findings highlight a distinctive mode of self-assembly for ubiquitin-like proteins and suggest that Ca-mediated ubiquitin-like protein filament assembly and/or disassembly enables cells to sense and respond to stress conditions that alter intracellular metal ion concentration.
History
DepositionAug 13, 2024-
Header (metadata) releaseApr 2, 2025-
Map releaseApr 2, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_46576.png

Downloads & links

-
Map

FileDownload / File: emd_46576.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 320 pix.
= 299.2 Å		0.94 Å/pix.
x 320 pix.
= 299.2 Å		0.94 Å/pix.
x 320 pix.
= 299.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.935 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.31356135 - 0.85959077
Average (Standard dev.)0.0017705535 (±0.018874474)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 299.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_46576_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_46576_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Filament assembly of Citrobacter sp. ubiquitin-like (Ubl) protein...

EntireName: Filament assembly of Citrobacter sp. ubiquitin-like (Ubl) protein with Ca ion
Components
  • Complex: Filament assembly of Citrobacter sp. ubiquitin-like (Ubl) protein with Ca ion
    • Protein or peptide: Multi-ubiquitin domain-containing protein
  • Ligand: CALCIUM ION

-
Supramolecule #1: Filament assembly of Citrobacter sp. ubiquitin-like (Ubl) protein...

SupramoleculeName: Filament assembly of Citrobacter sp. ubiquitin-like (Ubl) protein with Ca ion
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Citrobacter sp. RHBSTW-00271 (bacteria)
Molecular weightTheoretical: 20 kDa/nm

-
Macromolecule #1: Multi-ubiquitin domain-containing protein

MacromoleculeName: Multi-ubiquitin domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Citrobacter sp. RHBSTW-00271 (bacteria)
Molecular weightTheoretical: 28.376852 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKSSHHHHHH ENLYFQSNAQ DIQSQHHHRR FIEVADETLS FRQVVMEDST PNGSQISAAS GFKPDQMPVV LMLLPNGSLE DIRPDEVVD LSSEVRRFIV VESDRTYFFT IDGARLEWPC RFITGYSIRQ LGDIGDNKKL LLEREDEADL EVQNDQIIDL D GDGIERFI ...String:
MKSSHHHHHH ENLYFQSNAQ DIQSQHHHRR FIEVADETLS FRQVVMEDST PNGSQISAAS GFKPDQMPVV LMLLPNGSLE DIRPDEVVD LSSEVRRFIV VESDRTYFFT IDGARLEWPC RFITGYSIRQ LGDIGDNKKL LLEREDEADL EVQNDQIIDL D GDGIERFI SRKATWKLNI QGKEFTFDTP TVVIRDAVIR AGLNPNQAWH IFLKVEGQPK VEKNIDDVID LRTPGIEKLR LT PKDVNNG

-
Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 14 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 8.5
Component:
ConcentrationFormulaName
25.0 mMC4H11NO3Tris
300.0 mMNaClsodium chloride
5.0 mMMgCl2Calcium
1.0 mMC4H10O2S2DTT
5.0 percentC3H8O3glycerol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK III

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 27.912 Å
Applied symmetry - Helical parameters - Δ&Phi: -55.311 °
Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 629161
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
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