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- PDB-6sz9: Type IV Coupling Complex (T4CC) from L. pneumophila. -

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Basic information

Entry
Database: PDB / ID: 6sz9
TitleType IV Coupling Complex (T4CC) from L. pneumophila.
Components
  • DotY
  • DotZ
  • IcmJ (DotN)
  • IcmO (DotL)
  • IcmP (DotM)
KeywordsMEMBRANE PROTEIN / Protein Complex / Secretion / Secretion systems / Gram-negative bacteria / type 4 secretion system / T4SS / coupling protein / T4CC / DotL / DotM / DotN / DotY / DotZ
Function / homology
Function and homology information


protein transport / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
: / : / : / TraD/TraG, TraM recognition site / TraM recognition site of TraD and TraG / : / : / HNH nucleases / HNH nuclease / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Type 4 apparatus protein DotZ / Type 4 apparatus protein DotN / Type 4 coupling protein DotL / Type 4 apparatus protein DotM / Type 4 apparatus protein DotY
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsMace, K. / Meir, A. / Lukoyanova, N. / Waksman, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council321630 United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: Mechanism of effector capture and delivery by the type IV secretion system from Legionella pneumophila.
Authors: Amit Meir / Kevin Macé / Natalya Lukoyanova / David Chetrit / Manuela K Hospenthal / Adam Redzej / Craig Roy / Gabriel Waksman /
Abstract: Legionella pneumophila is a bacterial pathogen that utilises a Type IV secretion (T4S) system to inject effector proteins into human macrophages. Essential to the recruitment and delivery of ...Legionella pneumophila is a bacterial pathogen that utilises a Type IV secretion (T4S) system to inject effector proteins into human macrophages. Essential to the recruitment and delivery of effectors to the T4S machinery is the membrane-embedded T4 coupling complex (T4CC). Here, we purify an intact T4CC from the Legionella membrane. It contains the DotL ATPase, the DotM and DotN proteins, the chaperone module IcmSW, and two previously uncharacterised proteins, DotY and DotZ. The atomic resolution structure reveals a DotLMNYZ hetero-pentameric core from which the flexible IcmSW module protrudes. Six of these hetero-pentameric complexes may assemble into a 1.6-MDa hexameric nanomachine, forming an inner membrane channel for effectors to pass through. Analysis of multiple cryo EM maps, further modelling and mutagenesis provide working models for the mechanism for binding and delivery of two essential classes of Legionella effectors, depending on IcmSW or DotM, respectively.
History
DepositionOct 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Structure summary / Category: audit_author
Revision 1.2Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 23, 2022Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Jul 10, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-10350
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Structure viewerMolecule:
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Assembly

Deposited unit
A: IcmO (DotL)
B: IcmP (DotM)
C: IcmJ (DotN)
D: DotZ
E: DotY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,7276
Polymers214,6615
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area18540 Å2
ΔGint-102 kcal/mol
Surface area55320 Å2
MethodPISA

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Components

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Protein , 5 types, 5 molecules ABCDE

#1: Protein IcmO (DotL)


Mass: 87600.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal Streptavidin tag / Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: icmO, lpg0446 / Production host: Legionella pneumophila (bacteria) / References: UniProt: Q5ZYC6
#2: Protein IcmP (DotM)


Mass: 43858.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: icmP, lpg0445 / Production host: Legionella pneumophila (bacteria) / References: UniProt: Q5ZYC7
#3: Protein IcmJ (DotN)


Mass: 23762.971 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: icmJ, lpg0455 / Production host: Legionella pneumophila (bacteria) / References: UniProt: Q5ZYB7
#4: Protein DotZ


Mass: 33887.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: lpg1549 / Production host: Legionella pneumophila (bacteria) / References: UniProt: Q5ZV91
#5: Protein DotY


Mass: 25550.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: lpg0294 / Production host: Legionella pneumophila (bacteria) / References: UniProt: Q5ZYR7

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Non-polymers , 1 types, 1 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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: Coupling complex of the type IV secretion system / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Legionella pneumophila (bacteria)
Source (recombinant)Organism: Legionella pneumophila (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
10.2 Msodium chlorideNaCl1
250 mMtris aminomethane hydrochlorideTris-HCl1
320 mMMagnesium sulfateMgSO41
41 mMEthylenediaminetetraacetic acidEDTA1
SpecimenConc.: 0.175 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: UltrAuFoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 94 %

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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: OTHER
Image recordingElectron dose: 54 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 48

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Processing

EM software
IDNameVersionCategory
1Gautomatch0.56particle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7Coot0.8.9.1model fitting
9RELION3initial Euler assignment
11RELION3classification
12cryoSPARC23D reconstruction
13PHENIX1.14model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 219593 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT

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