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- PDB-8dql: CryoEM structure of IglD -

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Basic information

Entry
Database: PDB / ID: 8dql
TitleCryoEM structure of IglD
ComponentsSecretion system protein
KeywordsPROTEIN TRANSPORT / T6SS / baseplate
Function / homologyType VI secretion system TssK / Intracellular growth locus
Function and homology information
Biological speciesFrancisella tularensis subsp. novicida (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsLiu, X. / Clemens, D. / Lee, B. / Yang, X. / Zhou, H. / Horwitz, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI151055 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 United States
CitationJournal: mBio / Year: 2022
Title: Atomic Structure of IglD Demonstrates Its Role as a Component of the Baseplate Complex of the Type VI Secretion System.
Authors: Xiaoyu Liu / Daniel L Clemens / Bai-Yu Lee / Xue Yang / Z Hong Zhou / Marcus A Horwitz /
Abstract: Francisella tularensis, a Tier 1 select agent of bioterrorism, contains a type VI secretion system (T6SS) encoded within the pathogenicity island (FPI), which is critical for its pathogenesis. Among ...Francisella tularensis, a Tier 1 select agent of bioterrorism, contains a type VI secretion system (T6SS) encoded within the pathogenicity island (FPI), which is critical for its pathogenesis. Among the 18 proteins encoded by FPI is IglD, which is essential to 's intracellular growth and virulence, but neither its location within T6SS nor its functional role has been established. Here, we present the cryoEM structure of IglD from Francisella novicida and show that the IglD forms a homotrimer that is structurally homologous to the T6SS baseplate protein TssK in Escherichia coli. Each IglD monomer consists of an N-terminal β-sandwich domain, a 4-helix bundle domain, and a flexible C-terminal domain. While the overall folds of IglD and TssK are similar, the two structures differ in three aspects: the relative orientation between their β-sandwich and the 4-helix bundle domains; two insertion loops present in TssK's β-sandwich domain; and, consequently, a lack of subunit-subunit interaction between insertion loops in the IglD trimer. Phylogenetic analysis indicates that IglD is genetically remote from the TssK orthologs in other T6SSs. While the other components of the baseplate are unknown, we conducted pulldown assays showing IglJ interacts with IglD and IglH, pointing to a model wherein IglD, IglH, and IglJ form the baseplate of the T6SS. Alanine substitution mutagenesis further established that IglD's hydrophobic pocket in the N-terminal β-sandwich domain interacts with two loops of IglJ, reminiscent of the TssK-TssG interaction. These results form a framework for understanding the hitherto unexplored T6SS baseplate. Francisella tularensis is a facultatively intracellular Gram-negative bacterium that causes the serious and potentially fatal zoonotic illness, tularemia. Because of its extraordinarily high infectivity and mortality to humans, especially when inhaled, F. tularensis is considered a potential bioterrorism agent and is classified as a Tier 1 select agent. The type VI secretion system (T6SS) encoded within the pathogenicity island (FPI) is critical to its pathogenesis, but its baseplate components are largely unknown. Here, we report the cryoEM structure of IglD from Francisella novicida and demonstrate its role as a component of the baseplate complex of the T6SS. We further show that IglD interacts with IglJ and IglH, and propose a model in which these proteins interact to form the T6SS baseplate. Elucidation of the structure and composition of the baseplate should facilitate the design of strategies to prevent and treat infections caused by F. tularensis.
History
DepositionJul 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Secretion system protein
A: Secretion system protein
B: Secretion system protein


Theoretical massNumber of molelcules
Total (without water)148,6873
Polymers148,6873
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Secretion system protein / Intracellular growth locus


Mass: 49562.379 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. novicida (bacteria)
Gene: FNC33_03540
Production host: Francisella tularensis subsp. novicida (bacteria)
References: UniProt: A0A6I4RY94
Has protein modificationN

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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: IglD trimer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Francisella tularensis subsp. novicida (bacteria)
Source (recombinant)Organism: Francisella tularensis subsp. novicida (bacteria)
Buffer solutionpH: 7.4
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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 1800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1138462 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026522
ELECTRON MICROSCOPYf_angle_d0.4668802
ELECTRON MICROSCOPYf_dihedral_angle_d3.151843
ELECTRON MICROSCOPYf_chiral_restr0.0381014
ELECTRON MICROSCOPYf_plane_restr0.0021098

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