3WZ4

Structure of the periplasmic domain of DotI (crystal form I)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Molecular and structural analysis of Legionella DotI gives insights into an inner membrane complex essential for type IV secretion

Kuroda, T., Kubori, T., Thanh Bui, X., Hyakutake, A., Uchida, Y., Imada, K., Nagai, H.

(2015) Sci Rep 5: 10912-10912

  • DOI: 10.1038/srep10912
  • Primary Citation of Related Structures:  
    3WZ3, 3WZ4, 3WZ5

  • PubMed Abstract: 

    • The human pathogen Legionella pneumophila delivers a large array of the effector proteins into host cells using the Dot/Icm type IVB secretion system. Among the proteins composing the Dot/Icm system, an inner membrane protein DotI is known to be crucial for the secretion function but its structure and role in type IV secretion had not been elucidated ...

    The human pathogen Legionella pneumophila delivers a large array of the effector proteins into host cells using the Dot/Icm type IVB secretion system. Among the proteins composing the Dot/Icm system, an inner membrane protein DotI is known to be crucial for the secretion function but its structure and role in type IV secretion had not been elucidated. We report here the crystal structures of the periplasmic domains of DotI and its ortholog in the conjugation system of plasmid R64, TraM. These structures reveal a striking similarity to VirB8, a component of type IVA secretion systems, suggesting that DotI/TraM is the type IVB counterpart of VirB8. We further show that DotI and its partial paralog DotJ form a stable heterocomplex. R64 TraM, encoded by the conjugative plasmid lacking DotJ ortholog, forms a homo-hexamer. The DotI-DotJ complex is distinct from the core complex, which spans both inner and outer membranes to form a substrate conduit, and seems not to stably associate with the core complex. These results give insight into VirB8-family inner membrane proteins essential for type IV secretion and aid towards understanding the molecular basis of secretion systems essential for bacterial pathogenesis.

    Organizational Affiliation: 

    Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DotI
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
144Legionella pneumophilaMutation(s): 0 
Gene Names: dotI, icmL, C3927_01535, DIZ50_13030, ERS253277_01367, NCTC12000_00583
UniProt
Find proteins for O54626 (Legionella pneumophila)
Explore O54626 
Go to UniProtKB:  O54626
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO54626
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD
Download Ideal Coordinates CCD File 
AA [auth E],
BA [auth E],
EA [auth F],
FA [auth F],
IA [auth G],
AA [auth E],
BA [auth E],
EA [auth F],
FA [auth F],
IA [auth G],
JA [auth G],
K [auth A],
L [auth A],
MA [auth H],
NA [auth H],
O [auth B],
P [auth B],
S [auth C],
T [auth C],
W [auth D],
X [auth D]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N		 Ligand Interaction
MRD
Query on MRD
Download Ideal Coordinates CCD File 
CA [auth F],
DA [auth F],
GA [auth G],
HA [auth G],
I [auth A],
CA [auth F],
DA [auth F],
GA [auth G],
HA [auth G],
I [auth A],
J [auth A],
KA [auth H],
LA [auth H],
M [auth B],
N [auth B],
Q [auth C],
R [auth C],
U [auth D],
V [auth D],
Y [auth E],
Z [auth E]
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.59α = 90
b = 207.577β = 90
c = 58.179γ = 90
Software Package:
Software NamePurpose
SPring-8data collection
PHENIXmodel building
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2016-06-29
    Changes: Database references