+Open data
-Basic information
Entry | Database: PDB / ID: 7kmt | |||||||||||||||||||||||||||||||||
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Title | Structure of the yeast TRAPPIII-Ypt1(Rab1) complex | |||||||||||||||||||||||||||||||||
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Keywords | PROTEIN TRANSPORT / GTPase / GEF / ER / Golgi / Autophagy | |||||||||||||||||||||||||||||||||
Function / homology | Function and homology information pre-mRNA catabolic process / autophagy of peroxisome / Cvt vesicle assembly / Golgi Cisternae Pericentriolar Stack Reorganization / Golgi vesicle docking / regulation of endoplasmic reticulum unfolded protein response / Golgi vesicle budding / RAB geranylgeranylation / TRAPPI protein complex / SNARE complex disassembly ...pre-mRNA catabolic process / autophagy of peroxisome / Cvt vesicle assembly / Golgi Cisternae Pericentriolar Stack Reorganization / Golgi vesicle docking / regulation of endoplasmic reticulum unfolded protein response / Golgi vesicle budding / RAB geranylgeranylation / TRAPPI protein complex / SNARE complex disassembly / RAB GEFs exchange GTP for GDP on RABs / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / early endosome to Golgi transport / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPII-mediated vesicle transport / COPII-coated vesicle budding / cis-Golgi network membrane / cytoplasm to vacuole targeting by the Cvt pathway / protein localization to phagophore assembly site / phagophore assembly site membrane / intra-Golgi vesicle-mediated transport / Golgi stack / piecemeal microautophagy of the nucleus / endocytic recycling / cis-Golgi network / protein-containing complex localization / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / retrograde transport, endosome to Golgi / phagophore assembly site / cellular response to nitrogen starvation / SNARE complex assembly / reticulophagy / sporulation resulting in formation of a cellular spore / positive regulation of macroautophagy / autophagosome assembly / chromosome organization / endomembrane system / endoplasmic reticulum to Golgi vesicle-mediated transport / meiotic cell cycle / Neutrophil degranulation / SNARE binding / macroautophagy / intracellular protein transport / trans-Golgi network / cytoplasmic vesicle / protein-containing complex assembly / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / Golgi apparatus / endoplasmic reticulum / mitochondrion / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||||||||||||||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||||||||||||||||||||||||||
Authors | Joiner, A.M.N. / Phillips, B.P. / Miller, E.A. / Fromme, J.C. | |||||||||||||||||||||||||||||||||
Funding support | United States, United Kingdom, 10items
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Citation | Journal: EMBO J / Year: 2021 Title: Structural basis of TRAPPIII-mediated Rab1 activation. Authors: Aaron Mn Joiner / Ben P Phillips / Kumar Yugandhar / Ethan J Sanford / Marcus B Smolka / Haiyuan Yu / Elizabeth A Miller / J Christopher Fromme / Abstract: The GTPase Rab1 is a master regulator of the early secretory pathway and is critical for autophagy. Rab1 activation is controlled by its guanine nucleotide exchange factor, the multisubunit TRAPPIII ...The GTPase Rab1 is a master regulator of the early secretory pathway and is critical for autophagy. Rab1 activation is controlled by its guanine nucleotide exchange factor, the multisubunit TRAPPIII complex. Here, we report the 3.7 Å cryo-EM structure of the Saccharomyces cerevisiae TRAPPIII complex bound to its substrate Rab1/Ypt1. The structure reveals the binding site for the Rab1/Ypt1 hypervariable domain, leading to a model for how the complex interacts with membranes during the activation reaction. We determined that stable membrane binding by the TRAPPIII complex is required for robust activation of Rab1/Ypt1 in vitro and in vivo, and is mediated by a conserved amphipathic α-helix within the regulatory Trs85 subunit. Our results show that the Trs85 subunit serves as a membrane anchor, via its amphipathic helix, for the entire TRAPPIII complex. These findings provide a structural understanding of Rab activation on organelle and vesicle membranes. | |||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7kmt.cif.gz | 344 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kmt.ent.gz | 278.9 KB | Display | PDB format |
PDBx/mmJSON format | 7kmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kmt_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7kmt_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7kmt_validation.xml.gz | 61.8 KB | Display | |
Data in CIF | 7kmt_validation.cif.gz | 93.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/7kmt ftp://data.pdbj.org/pub/pdb/validation_reports/km/7kmt | HTTPS FTP |
-Related structure data
Related structure data | 22928MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
-Trafficking protein particle complex subunit ... , 6 types, 7 molecules HJGIFEK
#1: Protein | Mass: 24889.262 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: TRS23, YDR246W, YD8419.13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03784 | ||||
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#2: Protein | Mass: 31755.689 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: TRS31, YDR472W / Production host: Escherichia coli (E. coli) / References: UniProt: Q03337 | ||||
#3: Protein | Mass: 18453.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: BET5, YML077W / Production host: Escherichia coli (E. coli) / References: UniProt: Q03630 | ||||
#4: Protein | Mass: 22152.445 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: BET3, YKR068C / Production host: Escherichia coli (E. coli) / References: UniProt: P36149 #5: Protein | | Mass: 30786.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: TRS33, YOR115C, O3251, YOR3251C / Production host: Escherichia coli (E. coli) / References: UniProt: Q99394 #6: Protein | | Mass: 19721.154 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: TRS20, YBR254C, YBR1722 / Production host: Escherichia coli (E. coli) / References: UniProt: P38334 |
-Protein , 2 types, 2 molecules AB
#7: Protein | Mass: 23240.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: YPT1, YP2, YFL038C / Production host: Escherichia coli (E. coli) / References: UniProt: P01123 |
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#8: Protein | Mass: 82850.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: TRS85, GSG1, MUM1, YDR108W, YD9727.04 / Production host: Escherichia coli (E. coli) / References: UniProt: P46944 |
-Non-polymers , 1 types, 2 molecules
#9: Chemical |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: TRAPPIII-Ypt1 complex / Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT | ||||||||||||||||
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 | ||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K Details: Either 0.02% Tween-20 or 0.025% amphipol A8-35 was added before application of the sample to the grid. |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company / Model: Titan Krios / Image courtesy: FEI Company | ||||||||||||||||||||||||||||
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EM imaging |
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Image recording |
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EM imaging optics |
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-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 69315 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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