6SZ9

Type IV Coupling Complex (T4CC) from L. pneumophila.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mechanism of effector capture and delivery by the type IV secretion system from Legionella pneumophila.

Meir, A.Mace, K.Lukoyanova, N.Chetrit, D.Hospenthal, M.K.Redzej, A.Roy, C.Waksman, G.

(2020) Nat Commun 11: 2864-2864

  • DOI: https://doi.org/10.1038/s41467-020-16681-z
  • Primary Citation of Related Structures:  
    6SZ9

  • PubMed 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 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.


  • Organizational Affiliation

    Institute of Structural and Molecular Biology, Birkbeck and UCL, Malet Street, London, WC1E 7HX, UK. a.meir@mail.cryst.bbk.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IcmO (DotL)783Legionella pneumophilaMutation(s): 0 
Gene Names: icmOlpg0446
UniProt
Find proteins for Q5ZYC6 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZYC6 
Go to UniProtKB:  Q5ZYC6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZYC6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
IcmP (DotM)380Legionella pneumophilaMutation(s): 0 
Gene Names: icmPlpg0445
UniProt
Find proteins for Q5ZYC7 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZYC7 
Go to UniProtKB:  Q5ZYC7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZYC7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
IcmJ (DotN)208Legionella pneumophilaMutation(s): 0 
Gene Names: icmJlpg0455
UniProt
Find proteins for Q5ZYB7 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZYB7 
Go to UniProtKB:  Q5ZYB7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZYB7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DotZ294Legionella pneumophilaMutation(s): 0 
Gene Names: lpg1549
UniProt
Find proteins for Q5ZV91 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZV91 
Go to UniProtKB:  Q5ZV91
Entity Groups  
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UniProt GroupQ5ZV91
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DotY230Legionella pneumophilaMutation(s): 0 
Gene Names: lpg0294
UniProt
Find proteins for Q5ZYR7 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZYR7 
Go to UniProtKB:  Q5ZYR7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZYR7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
F [auth C]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2
MODEL REFINEMENTPHENIX1.14

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilUnited Kingdom321630

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 1.1: 2020-05-27
    Changes: Structure summary
  • Version 1.2: 2020-07-01
    Changes: Database references
  • Version 1.3: 2022-11-23
    Changes: Database references