7EA3

Intact Ypt32-TRAPPII (dimer).


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.31 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for assembly of TRAPPII complex and specific activation of GTPase Ypt31/32.

Mi, C.Zhang, L.Huang, G.Shao, G.Yang, F.You, X.Dong, M.Q.Sun, S.Sui, S.F.

(2022) Sci Adv 8: eabi5603-eabi5603

  • DOI: https://doi.org/10.1126/sciadv.abi5603

  • PubMed 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 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.


  • Organizational Affiliation

    State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRAPP-associated protein TCA17A,
M [auth N]
152Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TCA17YEL048CSYGP-ORF36
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Trafficking protein particle complex subunit 33B,
N [auth O]
268Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TRS33YOR115CO3251YOR3251C
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Trafficking protein particle complex subunit BET3C,
F,
O [auth P],
R [auth S]
193Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BET3YKR068C
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Trafficking protein particle complex subunit BET5D,
P [auth Q]
154Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BET5YML077W
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Trafficking protein particle complex subunit 23E,
Q [auth R]
219Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TRS23YDR246WYD8419.13
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Trafficking protein particle complex subunit 31G,
S [auth T]
283Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TRS31YDR472W
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Trafficking protein particle complex subunit 20H,
T [auth U]
175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TRS20YBR254CYBR1722
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Trafficking protein particle complex II-specific subunit 130I,
U [auth V]
1,102Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TRS130YMR218CYM8261.12C
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Trafficking protein particle complex II-specific subunit 120J,
V [auth W]
1,289Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TRS120YDR407CD9509.25ESBP10
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Trafficking protein particle complex II-specific subunit 65K,
W [auth X]
560Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TRS65KRE11YGR166W
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding protein YPT32/YPT11L,
X [auth Y]
222Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YPT32YPT11YGL210W
UniProt
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.31 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-09
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references