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- EMDB-46576: Structure of Citrobacter multi-ubiquitin protein filament -

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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-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46576.png

Downloads & links

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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
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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

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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 °

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Supplemental data

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Half map: #2

Fileemd_46576_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #1

Fileemd_46576_half_map_2.map
Projections & Slices
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Sample components

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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

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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

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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

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Macromolecule #2: CALCIUM ION

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

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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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

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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

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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
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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