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Open data
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Basic information
Entry | Database: PDB / ID: 7e8t | ||||||
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Title | Monomer of Ypt32-TRAPPII | ||||||
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Function / homology | ![]() 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 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mi, C.C. / Sui, S.F. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural basis for assembly of TRAPPII complex and specific activation of GTPase Ypt31/32. Authors: Chenchen Mi / Li Zhang / Guoqiang Huang / Guangcan Shao / Fan Yang / Xin You / Meng-Qiu Dong / Shan Sun / Sen-Fang Sui / ![]() Abstract: Transport protein particle (TRAPP) complexes belong to the multiprotein tethering complex and exist in three forms-core TRAPP/TRAPPI, TRAPPII, and TRAPPIII. TRAPPII activates GTPase Ypt31/Ypt32 as ...Transport protein particle (TRAPP) complexes belong to the multiprotein tethering complex and exist in three forms-core TRAPP/TRAPPI, TRAPPII, and TRAPPIII. TRAPPII activates GTPase Ypt31/Ypt32 as the guanine nucleotide exchange factor in the trans-Golgi network to determine the maturation of Golgi cisternae into post-Golgi carriers in yeast. Here, we present cryo-EM structures of yeast TRAPPII in apo and Ypt32-bound states. All the structures show a dimeric architecture assembled by two triangle-shaped monomers, while the monomer in the apo state exhibits both open and closed conformations, and the monomer in the Ypt32-bound form only captures the closed conformation. Located in the interior of the monomer, Ypt32 binds with both core TRAPP/TRAPPI and Trs120 via its nucleotide-binding domain and binds with Trs31 via its hypervariable domain. Combined with functional analysis, the structures provide insights into the assembly of TRAPPII and the mechanism of the specific activation of Ypt31/Ypt32 by TRAPPII. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 637.6 KB | Display | ![]() |
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PDB format | ![]() | 480.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 31022MC ![]() 7e2cC ![]() 7e2dC ![]() 7e8sC ![]() 7e93C ![]() 7e94C ![]() 7ea3C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein , 2 types, 2 molecules LA
#1: Protein | Mass: 24548.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: YPT32, YPT11, YGL210W / Production host: ![]() ![]() ![]() |
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#9: Protein | Mass: 17371.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: TCA17, YEL048C, SYGP-ORF36 / Production host: ![]() ![]() ![]() |
-Trafficking protein particle complex II-specific subunit ... , 3 types, 3 molecules IJK
#2: Protein | Mass: 128225.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: TRS130, YMR218C, YM8261.12C / Production host: ![]() ![]() ![]() |
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#3: Protein | Mass: 147823.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: TRS120, YDR407C, D9509.25, ESBP10 / Production host: ![]() ![]() ![]() |
#4: Protein | Mass: 63434.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: TRS65, KRE11, YGR166W / Production host: ![]() ![]() ![]() |
-Trafficking protein particle complex subunit ... , 6 types, 7 molecules BGEHDFC
#5: Protein | Mass: 30786.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: TRS33, YOR115C, O3251, YOR3251C / Production host: ![]() ![]() ![]() |
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#6: Protein | Mass: 31743.639 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: TRS31, YDR472W / Production host: ![]() ![]() ![]() |
#7: Protein | Mass: 24889.262 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: TRS23, YDR246W, YD8419.13 / Production host: ![]() ![]() ![]() |
#8: Protein | Mass: 19721.154 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: TRS20, YBR254C, YBR1722 / Production host: ![]() ![]() ![]() |
#10: Protein | Mass: 18453.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: BET5, YML077W / Production host: ![]() ![]() ![]() |
#11: Protein | Mass: 22152.445 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: BET3, YKR068C / Production host: ![]() ![]() ![]() |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: Monomer of Ypt32-TRAPPII. / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Vitrification![]() | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81870 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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