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	Cryo-EM structure of a type IV secretion system.
Journal, issue, pages	Nature, Vol. 607, Issue 7917, Page 191-196, Year 2022
Publish date	Jun 22, 2022
Authors	Kévin Macé / Abhinav K Vadakkepat / Adam Redzej / Natalya Lukoyanova / Clasien Oomen / Nathalie Braun / Marta Ukleja / Fang Lu / Tiago R D Costa / Elena V Orlova / David Baker / Qian Cong / Gabriel Waksman /
PubMed Abstract	Bacterial conjugation is the fundamental process of unidirectional transfer of DNAs, often plasmid DNAs, from a donor cell to a recipient cell. It is the primary means by which antibiotic resistance ...Bacterial conjugation is the fundamental process of unidirectional transfer of DNAs, often plasmid DNAs, from a donor cell to a recipient cell. It is the primary means by which antibiotic resistance genes spread among bacterial populations. In Gram-negative bacteria, conjugation is mediated by a large transport apparatus-the conjugative type IV secretion system (T4SS)-produced by the donor cell and embedded in both its outer and inner membranes. The T4SS also elaborates a long extracellular filament-the conjugative pilus-that is essential for DNA transfer. Here we present a high-resolution cryo-electron microscopy (cryo-EM) structure of a 2.8 megadalton T4SS complex composed of 92 polypeptides representing 8 of the 10 essential T4SS components involved in pilus biogenesis. We added the two remaining components to the structural model using co-evolution analysis of protein interfaces, to enable the reconstitution of the entire system including the pilus. This structure describes the exceptionally large protein-protein interaction network required to assemble the many components that constitute a T4SS and provides insights on the unique mechanism by which they elaborate pili.
External links	Nature / PubMed:35732732 / PubMed Central
Methods	EM (single particle)
Resolution	2.6 - 9.2 Å
Structure data	12707 7o3j EMDB-12707: O-Layer C14 at 2.58A - Local refinement with C14 symmetry of the O-layer of the outer membrane core complex from the fully-assembled R388 type IV secretion system. PDB-7o3j: O-layer structure (TrwH/VirB7, TrwF/VirB9CTD, TrwE/VirB10CTD) of the outer membrane core complex from the fully-assembled R388 type IV secretion system determined by cryo-EM. Method: EM (single particle) / Resolution: 2.6 Å 12708 7o3t EMDB-12708: I-Layer C16 at 3.08A - Local refinement with C16 symmetry of I-layer of the outer membrane core complex from the fully-assembled R388 type IV secretion system. PDB-7o3t: I-layer structure (TrwF/VirB9NTD, TrwE/VirB10NTD) of the outer membrane core complex from the fully-assembled R388 type IV secretion system determined by cryo-EM. Method: EM (single particle) / Resolution: 3.1 Å 12709 7o3v EMDB-12709: Stalk C1 at 3.71A - Local refinement without symmetry of the Stalk complex from the fully-assembled R388 type IV secretion system. PDB-7o3v: Stalk complex structure (TrwJ/VirB5-TrwI/VirB6) from the fully-assembled R388 type IV secretion system determined by cryo-EM. Method: EM (single particle) / Resolution: 3.7 Å 12715 7o41 EMDB-12715: IMC-Arches C6 at 8.33A - Refinement with C6 symmetry of the Inner Membrane Complex (IMC) with the Arches from the fully-assembled R388 type IV secretion system. PDB-7o41: Hexameric composite model of the Inner Membrane Complex (IMC) with the Arches from the fully-assembled R388 type IV secretion system determined by cryo-EM. Method: EM (single particle) / Resolution: 7.6 Å 12716 7o42 EMDB-12716: Trimer of dimers TrwK/VirB4unbound C1 at 4.14A - Refinement without symmetry of TrwK/VirB4unbound trimer of dimers complex (with Hcp1) from the R388 type IV secretion system. PDB-7o42: TrwK/VirB4unbound trimer of dimers complex (with Hcp1) from the R388 type IV secretion system determined by cryo-EM. Method: EM (single particle) / Resolution: 4.1 Å 12717 7o43 EMDB-12717: Dimer TrwK/VirB4unbound C1 at 3.49A - Local refinement without symmetry of the TrwK/VirB4unbound dimer complex from the R388 type IV secretion system. PDB-7o43: TrwK/VirB4unbound dimer complex from R388 type IV secretion system determined by cryo-EM. Method: EM (single particle) / Resolution: 3.4 Å 12933 7oiu EMDB-12933: IMC protomer C1 at 3.75A - Local refinement without symmetry of the inner membrane complex (IMC) protomer from the fully-assembled R388 type IV secretion system. PDB-7oiu: Inner Membrane Complex (IMC) protomer structure (TrwM/VirB3, TrwK/VirB4, TrwG/VirB8tails) from the fully-assembled R388 type IV secretion system determined by cryo-EM. Method: EM (single particle) / Resolution: 3.7 Å EMDB-13765: OMCC C1 at 3.28A - Refinement without symmetry of the outer membrane core complex (O- and I-layer) from the fully-assembled R388 type IV secretion system. Method: EM (single particle) / Resolution: 3.61 Å EMDB-13766: Ab Initio model for IMC-Arches-Stalk from the fully-assembled R388 type IV secretion system determined by cryo-EM. Method: EM (single particle) / Resolution: 9.2 Å 13767 7q1v EMDB-13767: IMC-Arches-Stalk C1 at 6.18A - Refinement of the IMC, Arches and Stalk complex without symmetry from the fully-assembled R388 type IV secretion system. PDB-7q1v: Arches protomer (trimer of TrwG/VirB8peri) structure from the fully-assembled R388 type IV secretion system determined by cryo-EM. Method: EM (single particle) / Resolution: 6.18 Å EMDB-13768: Stalk C5 at 3.28A - Local refinement with C5 symmetry of the Stalk complex from the fully-assembled R388 type IV secretion system. Method: EM (single particle) / Resolution: 3.28 Å
Source	escherichia coli (E. coli) salmonella dublin (bacteria) pseudomonas aeruginosa (strain atcc 15692 / dsm 22644 / cip 104116 / jcm 14847 / lmg 12228 / 1c / prs 101 / pao1) (bacteria)
Keywords	MEMBRANE PROTEIN / type IV secretion system / type 4 secretion system / T4SS / O-layer / core complex / outer membrane complex / inner membrane / R388 plasmid / conjugation / bacterial secretion / secretion / secretion system / protein complex / VirB10 / VirB9 / VirB7 / TrwE / TrwF / TrwH / I-layer / stalk / stalk complex / VirB5 / VirB6 / TrwJ / TrwI / IMC / inner membrane complex / arches / periplasmic / VirB3 / VirB4 / VirB8 / TrwM / TrwK / TrwG / ATPase / Hcp / dimer