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- PDB-7e8t: Monomer of Ypt32-TRAPPII -

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Basic information

Entry
Database: PDB / ID: 7e8t
TitleMonomer of Ypt32-TRAPPII
Components
  • (Trafficking protein particle complex II-specific subunit ...) x 3
  • (Trafficking protein particle complex subunit ...) x 6
  • GTP-binding protein YPT32/YPT11
  • TRAPP-associated protein TCA17
KeywordsTRANSPORT PROTEIN / Complex
Function / homology
Function and homology information


Anchoring of the basal body to the plasma membrane / beta-glucan biosynthetic process / TRAPPI protein complex / RAB geranylgeranylation / 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 / TRAPPI protein complex / RAB geranylgeranylation / 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 / protein localization to phagophore assembly site / intra-Golgi vesicle-mediated transport / cellular bud neck / cis-Golgi network / protein-containing complex localization / phagophore assembly site / retrograde transport, endosome to Golgi / 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 / recycling endosome / cell wall organization / 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
Beta-Lactamase - #70 / TRAPP II complex, Trs120 / TRAPP II complex TRAPPC10, C-terminal / Trafficking protein particle complex II-specific subunit 65 / Trafficking protein particle complex subunit TRAPPC10/Trs130 / Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit / Trafficking protein particle complex subunit 10, TRAPPC10 / TRAPP trafficking subunit Trs65 IgD3 / Trafficking protein particle complex subunit 2 / Sedlin, N-terminal conserved region ...Beta-Lactamase - #70 / TRAPP II complex, Trs120 / TRAPP II complex TRAPPC10, C-terminal / Trafficking protein particle complex II-specific subunit 65 / Trafficking protein particle complex subunit TRAPPC10/Trs130 / Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit / Trafficking protein particle complex subunit 10, TRAPPC10 / TRAPP trafficking subunit Trs65 IgD3 / Trafficking protein particle complex subunit 2 / Sedlin, N-terminal conserved region / Trafficking protein particle complex subunit / Sybindin-like family / Sybindin-like family / TRAPP I complex, subunit 5 / TRAPP complex, Trs33 subunit / Bet3 family / Transport protein particle (TRAPP) component / Transport protein particle (TRAPP) component / : / NO signalling/Golgi transport ligand-binding domain superfamily / Longin-like domain superfamily / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Beta-Lactamase / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRAPP-associated protein TCA17 / Trafficking protein particle complex II-specific subunit 65 / Trafficking protein particle complex subunit BET3 / Trafficking protein particle complex subunit 20 / GTP-binding protein YPT32/YPT11 / Trafficking protein particle complex subunit 31 / Trafficking protein particle complex subunit BET5 / Trafficking protein particle complex II-specific subunit 130 / Trafficking protein particle complex subunit 23 / Trafficking protein particle complex II-specific subunit 120 / Trafficking protein particle complex subunit 33
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsMi, C.C. / Sui, S.F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2022
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
DepositionMar 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
L: GTP-binding protein YPT32/YPT11
I: Trafficking protein particle complex II-specific subunit 130
J: Trafficking protein particle complex II-specific subunit 120
K: Trafficking protein particle complex II-specific subunit 65
B: Trafficking protein particle complex subunit 33
G: Trafficking protein particle complex subunit 31
E: Trafficking protein particle complex subunit 23
H: Trafficking protein particle complex subunit 20
A: TRAPP-associated protein TCA17
D: Trafficking protein particle complex subunit BET5
F: Trafficking protein particle complex subunit BET3
C: Trafficking protein particle complex subunit BET3


Theoretical massNumber of molelcules
Total (without water)551,30112
Polymers551,30112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 2 molecules LA

#1: Protein GTP-binding protein YPT32/YPT11 / Rab GTPase YPT32


Mass: 24548.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: YPT32, YPT11, YGL210W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P51996
#9: Protein TRAPP-associated protein TCA17 / 17 kDa TRAPP complex-associated protein


Mass: 17371.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TCA17, YEL048C, SYGP-ORF36 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32613

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Trafficking protein particle complex II-specific subunit ... , 3 types, 3 molecules IJK

#2: Protein Trafficking protein particle complex II-specific subunit 130 / TRAPP II-specific subunit 130 / Transport protein particle 130 kDa subunit


Mass: 128225.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TRS130, YMR218C, YM8261.12C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03660
#3: Protein Trafficking protein particle complex II-specific subunit 120 / TRAPP II-specific subunit 120 / Transport protein particle 120 kDa subunit


Mass: 147823.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TRS120, YDR407C, D9509.25, ESBP10 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q04183
#4: Protein Trafficking protein particle complex II-specific subunit 65 / TRAPP II-specific subunit 65 / Beta-glucan synthesis-associated protein TRS65 / Killer toxin- ...TRAPP II-specific subunit 65 / Beta-glucan synthesis-associated protein TRS65 / Killer toxin-resistance protein 11 / Transport protein particle 65 kDa subunit


Mass: 63434.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TRS65, KRE11, YGR166W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32893

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Trafficking protein particle complex subunit ... , 6 types, 7 molecules BGEHDFC

#5: Protein Trafficking protein particle complex subunit 33 / TRAPP subunit 33 / Transport protein particle 33 kDa subunit


Mass: 30786.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TRS33, YOR115C, O3251, YOR3251C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q99394
#6: Protein Trafficking protein particle complex subunit 31 / TRAPP subunit 31 / Transport protein particle 31 kDa subunit


Mass: 31743.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TRS31, YDR472W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03337
#7: Protein Trafficking protein particle complex subunit 23 / TRAPP subunit 23 / Transport protein particle 23 kDa subunit


Mass: 24889.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TRS23, YDR246W, YD8419.13 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03784
#8: Protein Trafficking protein particle complex subunit 20 / TRAPP subunit 20 / Transport protein particle 20 kDa subunit


Mass: 19721.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TRS20, YBR254C, YBR1722 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38334
#10: Protein Trafficking protein particle complex subunit BET5 / TRAPP subunit BET5 / Transport protein particle 18 kDa subunit


Mass: 18453.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: BET5, YML077W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03630
#11: Protein Trafficking protein particle complex subunit BET3 / TRAPP subunit BET3 / Transport protein particle 22 kDa subunit


Mass: 22152.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: BET3, YKR068C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36149

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Monomer of Ypt32-TRAPPII. / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81870 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00625234
ELECTRON MICROSCOPYf_angle_d1.34134354
ELECTRON MICROSCOPYf_dihedral_angle_d20.9848450
ELECTRON MICROSCOPYf_chiral_restr0.0714110
ELECTRON MICROSCOPYf_plane_restr0.0074462

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