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Yorodumi- PDB-7u05: Structure of the yeast TRAPPII-Rab11/Ypt32 complex in the closed/... -
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-Basic information
Entry | Database: PDB / ID: 7u05 | |||||||||
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Title | Structure of the yeast TRAPPII-Rab11/Ypt32 complex in the closed/closed state (composite structure) | |||||||||
Components |
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Keywords | PROTEIN TRANSPORT / complex / GTPase / Guanosine Exchange Factor / GEF | |||||||||
Function / homology | Function and homology information Anchoring of the basal body to the plasma membrane / beta-glucan biosynthetic process / RAB geranylgeranylation / TRAPPI protein complex / RAB GEFs exchange GTP for GDP on RABs / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / early endosome to Golgi transport / COPII-mediated vesicle transport ...Anchoring of the basal body to the plasma membrane / beta-glucan biosynthetic process / RAB geranylgeranylation / TRAPPI protein complex / RAB GEFs exchange GTP for GDP on RABs / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / early endosome to Golgi transport / COPII-mediated vesicle transport / cis-Golgi network membrane / cytoplasm to vacuole targeting by the Cvt pathway / cellular bud neck / protein localization to phagophore assembly site / intra-Golgi vesicle-mediated transport / cis-Golgi network / protein-containing complex localization / retrograde transport, endosome to Golgi / phagophore assembly site / cellular response to nitrogen starvation / exocytosis / positive regulation of macroautophagy / chromosome organization / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / Neutrophil degranulation / macroautophagy / trans-Golgi network / cell wall organization / recycling endosome / autophagy / protein transport / protein-containing complex assembly / mitochondrial outer membrane / early endosome / endosome / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / endoplasmic reticulum / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Bagde, S.R. / Fromme, J.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Sci Adv / Year: 2022 Title: Structure of a TRAPPII-Rab11 activation intermediate reveals GTPase substrate selection mechanisms. Authors: Saket R Bagde / J Christopher Fromme / 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u05.cif.gz | 2.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7u05.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7u05.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7u05_validation.pdf.gz | 864 KB | Display | wwPDB validaton report |
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Full document | 7u05_full_validation.pdf.gz | 865.8 KB | Display | |
Data in XML | 7u05_validation.xml.gz | 174.9 KB | Display | |
Data in CIF | 7u05_validation.cif.gz | 282 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/7u05 ftp://data.pdbj.org/pub/pdb/validation_reports/u0/7u05 | HTTPS FTP |
-Related structure data
Related structure data | 26254MC 7u06C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Trafficking protein particle complex II-specific subunit ... , 5 types, 10 molecules MmCcBbAaNn
#1: Protein | Mass: 20613.320 Da / Num. of mol.: 2 / Fragment: N-terminal region / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) #2: Protein | Mass: 63434.473 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32893 #11: Protein | Mass: 128424.250 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03660 #12: Protein | Mass: 147823.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q04183 #13: Protein | Mass: 17889.996 Da / Num. of mol.: 2 / Fragment: N-terminal region / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
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-Protein , 2 types, 4 molecules DdLl
#3: Protein | Mass: 17371.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32613 #10: Protein | Mass: 25309.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: YPT32, YPT11, YGL210W / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Rosetta 2 / References: UniProt: P51996 |
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-Trafficking protein particle complex subunit ... , 6 types, 14 molecules EeFIfiGgHhJjKk
#4: Protein | Mass: 30786.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q99394 #5: Protein | Mass: 22152.445 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36149 #6: Protein | Mass: 18453.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03630 #7: Protein | Mass: 24889.262 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03784 #8: Protein | Mass: 31755.689 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03337 #9: Protein | Mass: 19721.154 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38334 |
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-Non-polymers , 1 types, 4 molecules
#14: Chemical | ChemComp-PLM / |
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-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-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: TRAPPII complex bound to Rab11/Ypt32 / Type: COMPLEX / Entity ID: #1-#13 / Source: MULTIPLE SOURCES | ||||||||||||||||||||||||
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Molecular weight | Value: 1.1 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3) | ||||||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 5.6 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: The sample was incubated on the grid for 10 seconds followed by blotting for 5 seconds before plunging in liquid ethane. |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 63000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 3.5 sec. / Electron dose: 53 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 3 / Num. of real images: 4998 / Details: Images were collected as 50 frame movies. |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Width: 5760 / Height: 4092 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 979187 | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 369488 Details: The composite map was generated by combining the consensus dimer map (EMD-26221) with focused refinement maps deposited in the entries EMD-26223, EMD-26224. EMD-26225, EMD-26226, EMD-26227, ...Details: The composite map was generated by combining the consensus dimer map (EMD-26221) with focused refinement maps deposited in the entries EMD-26223, EMD-26224. EMD-26225, EMD-26226, EMD-26227, EMD-26228, EMD-26229, EMD-26230, EMD-26231 and EMD-26232 using Combine Focused Maps in Phenix. Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL Details: Model was rebuilt in coot and refined using phenix.real_space_refine. | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 107.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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