7E2C

Monomer of TRAPPII (open)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.18 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: 10.1126/sciadv.abi5603
  • Primary Citation of Related Structures:  
    7E2C, 7E2D, 7E8S, 7E8T, 7E93, 7E94, 7EA3

  • 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 ...

    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

    Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRAPP-associated protein TCA17A152Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TCA17YEL048CSYGP-ORF36
UniProt
Find proteins for P32613 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32613 
Go to UniProtKB:  P32613
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32613
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Trafficking protein particle complex subunit 33B268Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TRS33YOR115CO3251YOR3251C
UniProt
Find proteins for Q99394 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q99394 
Go to UniProtKB:  Q99394
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99394
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Trafficking protein particle complex subunit BET3C, F193Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BET3YKR068C
UniProt
Find proteins for P36149 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36149 
Go to UniProtKB:  P36149
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36149
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Trafficking protein particle complex subunit BET5D159Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BET5YML077W
UniProt
Find proteins for Q03630 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03630 
Go to UniProtKB:  Q03630
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03630
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Trafficking protein particle complex subunit 23E219Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TRS23YDR246WYD8419.13
UniProt
Find proteins for Q03784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03784 
Go to UniProtKB:  Q03784
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03784
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Trafficking protein particle complex subunit 31G283Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TRS31YDR472W
UniProt
Find proteins for Q03337 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03337 
Go to UniProtKB:  Q03337
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03337
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Trafficking protein particle complex subunit 20H175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TRS20YBR254CYBR1722
UniProt
Find proteins for P38334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38334 
Go to UniProtKB:  P38334
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38334
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Trafficking protein particle complex II-specific subunit 130I1,102Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TRS130YMR218CYM8261.12C
UniProt
Find proteins for Q03660 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03660 
Go to UniProtKB:  Q03660
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03660
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Trafficking protein particle complex II-specific subunit 120J1,289Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TRS120YDR407CD9509.25ESBP10
UniProt
Find proteins for Q04183 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04183 
Go to UniProtKB:  Q04183
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04183
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Trafficking protein particle complex II-specific subunit 65K559Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TRS65KRE11YGR166W
UniProt
Find proteins for P32893 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32893 
Go to UniProtKB:  P32893
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32893
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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