5X42

Structure of DotL(590-659)-DotN derived from Legionella pneumophila


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Architecture of the type IV coupling protein complex of Legionella pneumophila

Kwak, M.J.Kim, J.D.Kim, H.Kim, C.Bowman, J.W.Kim, S.Joo, K.Lee, J.Jin, K.S.Kim, Y.G.Lee, N.K.Jung, J.U.Oh, B.H.

(2017) Nat Microbiol 2: 17114-17114

  • DOI: https://doi.org/10.1038/nmicrobiol.2017.114
  • Primary Citation of Related Structures:  
    5X1E, 5X1H, 5X1U, 5X42, 5X90

  • PubMed Abstract: 

    Many bacteria, including Legionella pneumophila, rely on the type IV secretion system to translocate a repertoire of effector proteins into the hosts for their survival and growth. Type IV coupling protein (T4CP) is a hexameric ATPase that links translocating substrates to the transenvelope secretion conduit. Yet, how a large number of effector proteins are selectively recruited and processed by T4CPs remains enigmatic. DotL, the T4CP of L. pneumophila, contains an ATPase domain and a C-terminal extension whose function is unknown. Unlike T4CPs involved in plasmid DNA translocation, DotL appeared to function by forming a multiprotein complex with four other proteins. Here, we show that the C-terminal extension of DotL interacts with DotN, IcmS, IcmW and an additionally identified subunit LvgA, and that this pentameric assembly binds Legionella effector proteins. We determined the crystal structure of this assembly and built an architecture of the T4CP holocomplex by combining a homology model of the ATPase domain of DotL. The holocomplex is a hexamer of a bipartite structure composed of a membrane-proximal ATPase domain and a membrane-distal substrate-recognition assembly. The presented information demonstrates the architecture and functional dissection of the multiprotein T4CP complexes and provides important insights into their substrate recruitment and processing.


  • Organizational Affiliation

    Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DotN195Legionella pneumophilaMutation(s): 3 
Gene Names: dotNicmJERS240541_02347ERS253249_00846PtVF89_00655
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
IcmO (DotL)
B, D
70Legionella pneumophila subsp. pneumophila str. Philadelphia 1Mutation(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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
IcmJ (DotN)213Legionella pneumophila subsp. pneumophila str. Philadelphia 1Mutation(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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.683α = 90
b = 72.22β = 90
c = 170.435γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation of Korea (NRF)Korea, Republic Of2008-0061987

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references