4EYY | pdb_00004eyy

Crystal Structure of the IcmR-IcmQ complex from Legionella pneumophila


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.262 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4EYY

This is version 1.2 of the entry. See complete history

Literature

IcmQ in the Type 4b secretion system contains an NAD+ binding domain.

Farelli, J.D.Gumbart, J.C.Akey, I.V.Hempstead, A.Amyot, W.Head, J.F.McKnight, C.J.Isberg, R.R.Akey, C.W.

(2013) Structure 21: 1361-1373

  • DOI: https://doi.org/10.1016/j.str.2013.05.017
  • Primary Citation Related Structures: 
    4EYY

  • PubMed Abstract: 

    A Type 4b secretion system (T4bSS) is required for Legionella growth in alveolar macrophages. IcmQ associates with IcmR, binds to membranes, and has a critical role in the T4bSS. We have now solved a crystal structure of IcmR-IcmQ to further our understanding of this complex. This structure revealed an amphipathic four-helix bundle, formed by IcmR and the N-terminal domain of IcmQ, which is linked to a novel C-terminal domain of IcmQ (Qc) by a linker helix. The Qc domain has structural homology with ADP ribosyltransferase domains in certain bacterial toxins and binds NAD(+) with a dissociation constant in the physiological range. Structural homology and molecular dynamics were used to identify an extended NAD(+) binding site on Qc, and the resulting model was tested by mutagenesis and binding assays. Based on the data, we suggest that IcmR-IcmQ binds to membranes, where it may interact with, or perhaps modify, a protein in the T4bSS when NAD(+) is bound.


  • Organizational Affiliation
    • Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118-2526, USA.

Macromolecule Content 

  • Total Structure Weight: 34.48 kDa 
  • Atom Count: 2,038 
  • Modeled Residue Count: 247 
  • Deposited Residue Count: 311 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
IcmRA [auth R]120Legionella pneumophila subsp. pneumophila str. Philadelphia 1Mutation(s): 0 
Gene Names: icmRlpg0443
UniProt
Find proteins for Q5ZYC9 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZYC9 
Go to UniProtKB:  Q5ZYC9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZYC9
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
IcmQB [auth Q]191Legionella pneumophila str. CorbyMutation(s): 4 
Gene Names: icmQLPC_2899

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.262 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.948α = 90
b = 113.411β = 90
c = 49.465γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SHARPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2014-07-16
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references