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- PDB-9d5b: Structure of Methylobacterium brachiatum multi-ubiquitin protein ... -

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Basic information

Entry
Database: PDB / ID: 9d5b
TitleStructure of Methylobacterium brachiatum multi-ubiquitin protein filament
ComponentsMulti-ubiquitin domain-containing protein
KeywordsPROTEIN BINDING / ubiquitin / filament / beta-grasp
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsGong, M. / Gu, Y. / Corbett, K.D.
Funding support United States, 1items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multi-ubiquitin domain-containing protein
B: Multi-ubiquitin domain-containing protein
C: Multi-ubiquitin domain-containing protein
D: Multi-ubiquitin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,24714
Polymers116,8474
Non-polymers40110
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 10 through 155)
d_2ens_1(chain "B" and resid 10 through 155)
d_3ens_1(chain "C" and resid 10 through 155)
d_4ens_1(chain "D" and resid 10 through 155)

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 10 - 155 / Label seq-ID: 28 - 173

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC
d_4DD

NCS oper:
IDCodeMatrixVector
1given(-0.434779431829, 0.900534602535, -0.00206767878338), (0.900467013878, 0.434715888002, -0.0134630470888), (-0.0112250869406, -0.00771533250367, -0.999907231231)88.552525006, -53.4738687429, 299.982824264
2given(0.592321620889, 0.805700944492, 0.00104185983325), (0.805697004469, -0.592322109966, 0.00261821230856), (0.0027266127446, -0.000711400411713, -0.999996029738)-65.4178654309, 129.158219953, 266.768863095
3given(0.462706760371, 0.88634476876, -0.0171873441435), (-0.886399056326, 0.462869805343, 0.0069466715017), (0.0141126485839, 0.0120205737636, 0.999828154713)-54.9064845007, 233.433496645, -34.0640737519

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Components

#1: Protein
Multi-ubiquitin domain-containing protein


Mass: 29211.631 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacterium brachiatum (bacteria) / Gene: QO001_003913 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AAJ1WXN4
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Filament assembly of M. brachiatum ubiquitin-like (Ubl) protein with Ca ion
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 19.4 kDa/nm / Experimental value: NO
Source (natural)Organism: Methylobacterium brachiatum (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8.5
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTrisC4H11NO31
2300 mMsodium chlorideNaCl1
35 mMCalciumMgCl21
41 mMDTTC4H10O2S21
55 percentglycerolC3H8O31
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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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 magnification: 130000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 45 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -63.398 ° / Axial rise/subunit: 30.078 Å / Axial symmetry: D1
3D reconstructionResolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 159090 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 122.97 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00214752
ELECTRON MICROSCOPYf_angle_d0.40776480
ELECTRON MICROSCOPYf_chiral_restr0.0443732
ELECTRON MICROSCOPYf_plane_restr0.0031860
ELECTRON MICROSCOPYf_dihedral_angle_d9.56541728
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints5.44735362516E-11
ens_1d_3AAELECTRON MICROSCOPYNCS constraints2.74967977672E-13
ens_1d_4AAELECTRON MICROSCOPYNCS constraints7.15167642052E-12

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