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	Structure of a TRAPPII-Rab11 activation intermediate reveals GTPase substrate selection mechanisms.
Journal, issue, pages	Sci Adv, Vol. 8, Issue 19, Page eabn7446, Year 2022
Publish date	May 13, 2022
Authors	Saket R Bagde / J Christopher Fromme /
PubMed Abstract	Rab1 and Rab11 are essential regulators of the eukaryotic secretory and endocytic recycling pathways. The transport protein particle (TRAPP) complexes activate these guanosine triphosphatases via ...Rab1 and Rab11 are essential regulators of the eukaryotic secretory and endocytic recycling pathways. The transport protein particle (TRAPP) complexes activate these guanosine triphosphatases via nucleotide exchange using a shared set of core subunits. The basal specificity of the TRAPP core is toward Rab1, yet the TRAPPII complex is specific for Rab11. A steric gating mechanism has been proposed to explain TRAPPII counterselection against Rab1. Here, we present cryo-electron microscopy structures of the 22-subunit TRAPPII complex from budding yeast, including a TRAPPII-Rab11 nucleotide exchange intermediate. The Trs130 subunit provides a "leg" that positions the active site distal to the membrane surface, and this leg is required for steric gating. The related TRAPPIII complex is unable to activate Rab11 because of a repulsive interaction, which TRAPPII surmounts using the Trs120 subunit as a "lid" to enclose the active site. TRAPPII also adopts an open conformation enabling Rab11 to access and exit from the active site chamber.
External links	Sci Adv / PubMed:35559680 / PubMed Central
Methods	EM (single particle)
Resolution	3.4 - 9.2 Å
Structure data	EMDB-26221: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/closed state (consensus map of symmetric dimer) Method: EM (single particle) / Resolution: 4.1 Å EMDB-26223: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/closed state (focused refinement of closed monomer) Method: EM (single particle) / Resolution: 3.7 Å EMDB-26224: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/closed state (focused refinement of dimer interface) Method: EM (single particle) / Resolution: 3.5 Å EMDB-26225: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/closed state (focused refinement of central region of closed monomer) Method: EM (single particle) / Resolution: 3.5 Å EMDB-26226: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/closed state (focused refinement of core and Ypt32) Method: EM (single particle) / Resolution: 3.4 Å EMDB-26227: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/closed state (focused refinement of Ypt32 and region around Ypt32) Method: EM (single particle) / Resolution: 3.5 Å EMDB-26228: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/closed state (focused refinement of Trs130 N-terminal region, Tca17, Trs33 and Bet3) Method: EM (single particle) / Resolution: 3.7 Å EMDB-26229: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/closed state (focused refinement of Trs130 middle region, Tca17, Trs33 and Bet3) Method: EM (single particle) / Resolution: 3.7 Å EMDB-26230: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/closed state (focused refinement of Trs120 N-terminal region and Trs20) Method: EM (single particle) / Resolution: 3.5 Å EMDB-26231: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/closed state (focused refinement of Trs120 middle region) Method: EM (single particle) / Resolution: 3.7 Å EMDB-26232: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/closed state (focused refinement of Trs65 N-terminal region, Trs130 C-terminal region, Trs120 N-terminal region, Trs20, Trs31 and Bet3) Method: EM (single particle) / Resolution: 3.9 Å EMDB-26233: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/open state (consensus map of asymmetric dimer state A) Method: EM (single particle) / Resolution: 4.5 Å EMDB-26234: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/open state (focused refinement of open monomer) Method: EM (single particle) / Resolution: 4.2 Å EMDB-26235: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/open state (focused refinement of closed monomer in asymmetric dimer state A) Method: EM (single particle) / Resolution: 4.2 Å EMDB-26236: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/open state (focused refinement of dimer interface) Method: EM (single particle) / Resolution: 3.9 Å EMDB-26237: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/open state (focused refinement of Tca17, Trs33 and Bet3 in the open monomer) Method: EM (single particle) / Resolution: 3.9 Å EMDB-26238: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/open state (focused refinement of core in the open monomer) Method: EM (single particle) / Resolution: 3.8 Å EMDB-26239: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/open state (focused refinement of Trs120 N-terminal region and Trs20 in the open monomer) Method: EM (single particle) / Resolution: 3.8 Å EMDB-26240: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/open state (focused refinement of Trs120 middle region in the open monomer) Method: EM (single particle) / Resolution: 4.3 Å EMDB-26241: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/open state (focused refinement of central region in the open monomer) Method: EM (single particle) / Resolution: 3.9 Å EMDB-26242: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/open state (focused refinement of Trs130 middle region in the open monomer) Method: EM (single particle) / Resolution: 4.2 Å EMDB-26243: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/open state (focused refinement of Trs65 N-terminal region in the open monomer) Method: EM (single particle) / Resolution: 8.6 Å EMDB-26244: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/open state (focused refinement of Trs130 N-terminal region, Tca17, Trs33 and Bet3 in the open monomer) Method: EM (single particle) / Resolution: 4.3 Å EMDB-26245: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/open state (focused refinement of core and Ypt32 in the closed monomer) Method: EM (single particle) / Resolution: 3.9 Å EMDB-26246: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/open state (focused refinement of Trs120 N-terminal region and Trs20 in the closed monomer) Method: EM (single particle) / Resolution: 3.9 Å EMDB-26248: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/open state (focused refinement of Trs120 middle region in the closed monomer) Method: EM (single particle) / Resolution: 4.2 Å EMDB-26249: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/open state (focused refinement of central region of the closed monomer) Method: EM (single particle) / Resolution: 4.0 Å EMDB-26250: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/open state (focused refinement of Trs130 middle region in the closed monomer) Method: EM (single particle) / Resolution: 4.3 Å EMDB-26251: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/open state (focused refinement of Trs130 middle region, Tca17, Trs33 and Bet3 in the closed monomer) Method: EM (single particle) / Resolution: 4.2 Å EMDB-26252: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/open state (focused refinement of Trs130 N-terminal region, Tca17, Trs33 and Bet3 in the closed monomer) Method: EM (single particle) / Resolution: 4.2 Å EMDB-26253: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/open state (focused refinement of Trs65 N-terminal region in the closed monomer) Method: EM (single particle) / Resolution: 9.2 Å 26254 7u05 EMDB-26254, PDB-7u05: Structure of the yeast TRAPPII-Rab11/Ypt32 complex in the closed/closed state (composite structure) Method: EM (single particle) / Resolution: 3.7 Å 26255 7u06 EMDB-26255, PDB-7u06: Structure of the yeast TRAPPII-Rab11/Ypt32 complex in the closed/open state (composite structure) Method: EM (single particle) / Resolution: 4.2 Å EMDB-26269: Yeast TRAPPII complex in the closed/open state (consensus map) Method: EM (single particle) / Resolution: 4.7 Å EMDB-26270: Yeast TRAPPII complex in the closed/closed state (consensus map) Method: EM (single particle) / Resolution: 4.2 Å EMDB-26271: Yeast TRAPPII complex in the partially open/open state (consensus map) Method: EM (single particle) / Resolution: 4.9 Å EMDB-26272: Yeast TRAPPII complex in the closed/partially open (consensus map) Method: EM (single particle) / Resolution: 4.9 Å
Chemicals	ChemComp-PLM: PALMITIC ACID
Source	saccharomyces cerevisiae (brewer's yeast) Baker's yeast (brewer's yeast)
Keywords	PROTEIN TRANSPORT / complex / GTPase / Guanosine Exchange Factor / GEF