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- EMDB-34350: Legionella pneumophila Deubiquitinase, LotA(7-544) apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-34350
TitleLegionella pneumophila Deubiquitinase, LotA(7-544) apo state
Map data
Sample
  • Organelle or cellular component: Deubiquitinase of LotA 7-544 apo state
KeywordsDeubuiquitinase / OTU domain / SIGNALING PROTEIN
Biological speciesLegionella pneumophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.0 Å
AuthorsKang SW / Kim GH / Roh SH / Shin DH
Funding support Korea, Republic Of, 2 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1C1C100396112 Korea, Republic Of
National Research Foundation (NRF, Korea)2018R1A6A1A03025607 Korea, Republic Of
CitationJournal: Life Sci Alliance / Year: 2023
Title: Structural insights into ubiquitin chain cleavage by ovarian tumor deubiquitinases.
Authors: Sangwoo Kang / Gyuhee Kim / Minhyeong Choi / Minwoo Jeong / Gerbrand J van der Heden van Noort / Soung-Hun Roh / Donghyuk Shin /
Abstract: Although ubiquitin is found only in eukaryotes, several pathogenic bacteria and viruses possess proteins that hinder the host ubiquitin system. , a gram-negative intracellular bacterium, possesses an ...Although ubiquitin is found only in eukaryotes, several pathogenic bacteria and viruses possess proteins that hinder the host ubiquitin system. , a gram-negative intracellular bacterium, possesses an ovarian tumor (OTU) family of deubiquitinases (Lot DUBs). Herein, we describe the molecular characteristics of Lot DUBs. We elucidated the structure of the LotA OTU1 domain and revealed that entire Lot DUBs possess a characteristic extended helical lobe that is not found in other OTU-DUBs. The structural topology of an extended helical lobe is the same throughout the Lot family, and it provides an S1' ubiquitin-binding site. Moreover, the catalytic triads of Lot DUBs resemble those of the A20-type OTU-DUBs. Furthermore, we revealed a unique mechanism by which LotA OTU domains cooperate together to distinguish the length of the chain and preferentially cleave longer K48-linked polyubiquitin chains. The LotA OTU1 domain itself cleaves K6-linked ubiquitin chains, whereas it is also essential for assisting the cleavage of longer K48-linked polyubiquitin chains by the OTU2 domain. Thus, this study provides novel insights into the structure and mechanism of action of Lot DUBs.
History
DepositionSep 19, 2022-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34350.png

Downloads & links

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Map

FileDownload / File: emd_34350.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.68 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.0054583326 - 0.017749509
Average (Standard dev.)0.00018907696 (±0.001984588)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 136.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34350_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_34350_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Deubiquitinase of LotA 7-544 apo state

EntireName: Deubiquitinase of LotA 7-544 apo state
Components
  • Organelle or cellular component: Deubiquitinase of LotA 7-544 apo state

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Supramolecule #1: Deubiquitinase of LotA 7-544 apo state

SupramoleculeName: Deubiquitinase of LotA 7-544 apo state / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Legionella pneumophila (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.6 mg/mL
BufferpH: 7.6
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 3 seconds before plunging.
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.04 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: OTHER / Number images used: 176036
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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