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- PDB-9fgm: Cryo-EM structure of Legionella effector SdeC (3D flexible refinement) -

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Basic information

Entry
Database: PDB / ID: 9fgm
TitleCryo-EM structure of Legionella effector SdeC (3D flexible refinement)
ComponentsSdeC
KeywordsTOXIN / Phospho-ribose ubiquitination / mono-ADP ribosyl transferase / Phosphodiesterase / deubiquitinase
Function / homologySidE, DUB domain / SidE, mono-ADP-ribosyltransferase domain / SidE mono-ADP-ribosyltransferase domain / SidE DUB domain / SidE, PDE domain / SidE phosphodiesterase (PDE) domain / NAD+-protein-arginine ADP-ribosyltransferase activity / protein deubiquitination / SdeC
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsWeng, T.-H. / Misra, M. / Chen, W. / Safarian, S. / Kudryashev, M. / Dikic, I.
Funding supportEuropean Union, Germany, 2items
OrganizationGrant numberCountry
European Research Council (ERC)742720European Union
German Research Foundation (DFG)253130777 Germany
CitationJournal: To Be Published
Title: BAR-like C-terminal domain of Legionella SidE family is crucial for its membrane localization and secretion
Authors: Misra, M. / Mukherjee, R. / Bhattacharya, A. / Chen, W. / Weng, T.-H. / van Ek, L. / Cristiani, A. / Li, C. / Mohammed, A. / Liu, Y. / Pomirska, J. / Vidov, A. / Heden van Noort, G. / ...Authors: Misra, M. / Mukherjee, R. / Bhattacharya, A. / Chen, W. / Weng, T.-H. / van Ek, L. / Cristiani, A. / Li, C. / Mohammed, A. / Liu, Y. / Pomirska, J. / Vidov, A. / Heden van Noort, G. / Bhaskara, R. / Svergun, D. / Gavin, A.C. / Safarian, S. / Kudryashev, M. / Luo, Z.-Q. / Dikic, I.
History
DepositionMay 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 2.0Jun 11, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update
Revision 1.1Jun 18, 2025Group: Data collection / Category: em_admin / em_imaging
Item: _em_admin.last_update / _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min
Revision 2.1Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data collection / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_imaging / Data content type: EM metadata / EM metadata / EM metadata
Item: _em_admin.last_update / _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SdeC


Theoretical massNumber of molelcules
Total (without water)199,4711
Polymers199,4711
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein SdeC


Mass: 199470.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6RCQ8
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SdeC / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.199 MDa / Experimental value: YES
Source (natural)Organism: Legionella pneumophila (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 33 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
2PHENIX1.20.1_4487:model refinement
13cryoSPARC4.4.13D reconstruction3dflex
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1489769
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 149762
Details: The final refinement was done using cryoSPARC 3DFlex with an outer solvent mask that includes the whole protein.
Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310591
ELECTRON MICROSCOPYf_angle_d0.54214280
ELECTRON MICROSCOPYf_dihedral_angle_d4.6171398
ELECTRON MICROSCOPYf_chiral_restr0.0371600
ELECTRON MICROSCOPYf_plane_restr0.0041870

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