6EXE | pdb_00006exe

Crystal structure of DotM cytoplasmic domain (residues 153-380),R217E


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.264 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Legionella DotM structure reveals a role in effector recruiting to the Type 4B secretion system.

Meir, A.Chetrit, D.Liu, L.Roy, C.R.Waksman, G.

(2018) Nat Commun 9: 507-507

  • DOI: https://doi.org/10.1038/s41467-017-02578-x
  • Primary Citation Related Structures: 
    6EXA, 6EXB, 6EXC, 6EXD, 6EXE

  • PubMed Abstract: 

    Legionella pneumophila, a causative agent of pneumonia, utilizes the Type 4B secretion (T4BS) system to translocate over 300 effectors into the host cell during infection. T4BS systems are encoded by a large gene cluster termed dot/icm, three components of which, DotL, DotM, and DotN, form the "coupling complex", which serves as a platform for recruitment of effector proteins. One class of effectors includes proteins containing Glu-rich/E-block sequences at their C terminus. However, the protein or region of the coupling complex mediating recruitment of such effectors is unknown. Here we present the crystal structure of DotM. This all alpha-helical structure exhibits patches of positively charged residues. We show that these regions form binding sites for acidic Glu-rich peptides and that mutants targeting these patches are defective in vivo in the translocation of acidic Glu-rich motif-containing effectors. We conclude that DotM forms the interacting surface for recruitment of acidic Glu-rich motif-containing Legionella effectors.


  • Organizational Affiliation
    • Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, Malet Street, London, WC1E 7HX, UK.

Macromolecule Content 

  • Total Structure Weight: 53.62 kDa 
  • Atom Count: 3,721 
  • Modeled Residue Count: 442 
  • Deposited Residue Count: 470 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
IcmP (DotM)
A, B
235Legionella pneumophila subsp. pneumophila str. Philadelphia 1Mutation(s): 1 
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.264 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.278α = 90
b = 118.278β = 90
c = 66.571γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilUnited Kingdom321630

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2018-03-07
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description