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- EMDB-46578: Structure of Methylobacterium brachiatum multi-ubiquitin protein ... -

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Basic information

Entry
Database: EMDB / ID: EMD-46578
TitleStructure of Methylobacterium brachiatum multi-ubiquitin protein filament
Map data
Sample
  • Complex: Filament assembly of M. brachiatum ubiquitin-like (Ubl) protein with Ca ion
    • Protein or peptide: Multi-ubiquitin domain-containing protein
  • Ligand: CALCIUM ION
Keywordsubiquitin / filament / beta-grasp / PROTEIN BINDING
Function / homologyProtein of unknown function DUF2604 / Protein of Unknown function (DUF2604) / Multi-ubiquitin domain / Multiubiquitin / Multi-ubiquitin domain-containing protein
Function and homology information
Biological speciesMethylobacterium brachiatum (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.08 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_46578.png

Downloads & links

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Map

FileDownload / File: emd_46578.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 400 pix.
= 328.8 Å		0.82 Å/pix.
x 400 pix.
= 328.8 Å		0.82 Å/pix.
x 400 pix.
= 328.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.08616437 - 0.35463458
Average (Standard dev.)0.0008872007 (±0.011567377)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 328.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_46578_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_46578_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Filament assembly of M. brachiatum ubiquitin-like (Ubl) protein w...

EntireName: Filament assembly of M. brachiatum ubiquitin-like (Ubl) protein with Ca ion
Components
  • Complex: Filament assembly of M. brachiatum 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 M. brachiatum ubiquitin-like (Ubl) protein w...

SupramoleculeName: Filament assembly of M. brachiatum ubiquitin-like (Ubl) protein with Ca ion
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Methylobacterium brachiatum (bacteria)
Molecular weightTheoretical: 19.4 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: Methylobacterium brachiatum (bacteria)
Molecular weightTheoretical: 29.211631 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKSSHHHHHH ENLYFQSNAH EHEHVEDRVA VQVFDENLNA KDVHLTDPVP TGRQIIKAAG KHPVDDYAVL AWMPDNALRP LHLDETFDL RQHGVERILV APSDTLYRFF IDGQDQEWPV RGITGVVLKT LAGVDPAAFE VFLVIPGDDD IRVEDHELFD L ARKGVEHF ...String:
MKSSHHHHHH ENLYFQSNAH EHEHVEDRVA VQVFDENLNA KDVHLTDPVP TGRQIIKAAG KHPVDDYAVL AWMPDNALRP LHLDETFDL RQHGVERILV APSDTLYRFF IDGQDQEWPV RGITGVVLKT LAGVDPAAFE VFLVIPGDDD IRVEDHELFD L ARKGVEHF QTVKRKAPAE HGIALKVVVN GTETELKVHA GTPLRQVRTE ALQKSGNVGR PEDEWQLKDE HGNPYDLNQT VA GVGLHDG DLVWLSLNAG VAGV

UniProtKB: Multi-ubiquitin domain-containing protein

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 10 / 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
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: 30.078 Å
Applied symmetry - Helical parameters - Δ&Phi: -63.398 °
Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 159090
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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