Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	In situ structures of the Dot/Icm T4SS identify the DotA-IcmX complex as the gatekeeper for effector translocation.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 122, Issue 39, Page e2516300122, Year 2025
Publish date	Sep 30, 2025
Authors	Jian Yue / Samira Heydari / Donghyun Park / David Chetrit / Shoichi Tachiyama / Wangbiao Guo / Jack M Botting / Shenping Wu / Craig R Roy / Jun Liu /
PubMed Abstract	The Dot/Icm machine of is among the most versatile type IV secretion systems (T4SSs), capable of translocating more than 330 distinct effector proteins across the bacterial envelope into host cells. ...The Dot/Icm machine of is among the most versatile type IV secretion systems (T4SSs), capable of translocating more than 330 distinct effector proteins across the bacterial envelope into host cells. Assembly and function of the system require at least 27 Dot and Icm proteins, yet its architecture and activation mechanism remain poorly understood at the molecular level. Here, we deploy in situ single-particle cryoelectron microscopy to determine near-atomic structures of the Dot/Icm machine and its intimate association with three distinct outer membrane porins in intact bacteria. Notably, two essential yet enigmatic components, DotA and IcmX, form a pentameric protochannel in an inactive state at the central axis of the Dot/Icm machine. Upon Dot/Icm activation with host lysate, this protochannel undergoes extensive rearrangements to generate an extended transenvelope conduit, as visualized by cryoelectron tomography (cryo-ET) and subtomogram averaging. Furthermore, a combination of cryo-ET and cryo-FIB milling of macrophages infected with reveals tethering of the Dot/Icm machine to the host membrane, suggesting direct translocation of effector proteins from the bacterial cytoplasm into the host. Together, our studies identify the DotA-IcmX complex as a gatekeeper for effector translocation and provide a molecular framework for understanding the assembly and activation of the elaborate Dot/Icm T4SS.
External links	Proc Natl Acad Sci U S A / PubMed:40986344 / PubMed Central
Methods	EM (single particle)
Resolution	2.96 - 4.63 Å
Structure data	49393 9ngu EMDB-49393: In-situ cryo-EM structure of outer membrane cap (OMC) of the Dot/Icm machine PDB-9ngu: In situ cryo-EM structure of outer membrane cap (OMC) of the Legionella Dot/Icm T4SS machine Method: EM (single particle) / Resolution: 2.96 Å 49394 9ngv EMDB-49394: In-situ cryo-EM structure of periplasmic ring (PR) of the Dot/Icm machine PDB-9ngv: In situ cryo-EM structure of periplasmic ring (PR) of the Legionella Dot/Icm T4SS machine. Method: EM (single particle) / Resolution: 3.04 Å 49395 9ngw 9nh2 EMDB-49395: In-situ cryo-EM structure of Dome of the Dot/Icm machine PDB-9ngw: In-situ cryo-EM structure of Dome of the Legionella Dot/Icm machine PDB-9nh2: In situ cryo-EM structure of porin III of the Legionella Dot/Icm T4SS machine Method: EM (single particle) / Resolution: 3.08 Å 49396 9ngy EMDB-49396: In-situ cryo-EM structure of protochannel of the Dot/Icm machine PDB-9ngy: In situ cryo-EM structure of protochannel (DotA-IcmX) of the Legionella Dot/Icm T4SS machine Method: EM (single particle) / Resolution: 3.63 Å 49398 9nh0 EMDB-49398: In-situ cryo-EM structure of PR and DotA-IcmX of the Dot/Icm machine at C1 PDB-9nh0: In situ cryo-EM structure of PR and DotA-IcmX of the Legionella Dot/Icm T4SS machine at C1 symmetry Method: EM (single particle) / Resolution: 4.63 Å 49399 9nh1 EMDB-49399: In-situ cryo-EM structure of porinI of the Dot/Icm machine PDB-9nh1: In situ cryo-EM structure of porin I of the Legionella Dot/Icm T4SS machine Method: EM (single particle) / Resolution: 3.56 Å
Source	legionella pneumophila subsp. pneumophila (bacteria)
Keywords	PROTEIN TRANSPORT / Type IVB Dot/Icm Secretion Machine