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- PDB-7b70: TRAPPCore plus C8 (355-596) and C11 (1-718) from MiniTRAPPIII -

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Basic information

Entry
Database: PDB / ID: 7b70
TitleTRAPPCore plus C8 (355-596) and C11 (1-718) from MiniTRAPPIII
Components
  • (Trafficking protein particle complex ...) x 5
  • FI18195p1
  • GEO08327p1
  • Probable trafficking protein particle complex subunit 2
  • TRAPPC2L
KeywordsEXOCYTOSIS / Rab1 / GEFs / Golgi / TRAPP complexes
Function / homology
Function and homology information


COPII-mediated vesicle transport / RAB GEFs exchange GTP for GDP on RABs / TRAPPI protein complex / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / dsRNA transport / Golgi vesicle transport / Neutrophil degranulation / intra-Golgi vesicle-mediated transport ...COPII-mediated vesicle transport / RAB GEFs exchange GTP for GDP on RABs / TRAPPI protein complex / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / dsRNA transport / Golgi vesicle transport / Neutrophil degranulation / intra-Golgi vesicle-mediated transport / cis-Golgi network / cis-Golgi network membrane / intracellular transport / protein secretion / long-term memory / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / trans-Golgi network / spermatogenesis / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / nucleus / cytosol / cytoplasm
Similarity search - Function
Trafficking protein particle complex subunit 2-like / Trafficking protein particle complex subunit 11 / Trafficking protein particle complex subunit 11, C-terminal / Foie gras liver health family 1 / Gryzun, putative Golgi trafficking / TRAPP III complex, Trs85 / ER-Golgi trafficking TRAPP I complex 85 kDa subunit / Trafficking protein particle complex subunit 2 / Sedlin, N-terminal conserved region / Trafficking protein particle complex subunit ...Trafficking protein particle complex subunit 2-like / Trafficking protein particle complex subunit 11 / Trafficking protein particle complex subunit 11, C-terminal / Foie gras liver health family 1 / Gryzun, putative Golgi trafficking / TRAPP III complex, Trs85 / ER-Golgi trafficking TRAPP I complex 85 kDa subunit / 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
Similarity search - Domain/homology
Trafficking protein particle complex subunit 2-like protein / Trafficking protein particle complex subunit 5 / Trafficking protein particle complex subunit 11 / Trafficking protein particle complex subunit / GEO08327p1 / Trafficking protein particle complex subunit / Trafficking protein particle complex subunit / Probable trafficking protein particle complex subunit 2 / FI18195p1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsGalindo, A. / Munro, S. / Planelles-Herrero, V.J.
CitationJournal: EMBO J / Year: 2021
Title: Cryo-EM structure of metazoan TRAPPIII, the multi-subunit complex that activates the GTPase Rab1.
Authors: Antonio Galindo / Vicente J Planelles-Herrero / Gianluca Degliesposti / Sean Munro /
Abstract: The TRAPP complexes are nucleotide exchange factors that play essential roles in membrane traffic and autophagy. TRAPPII activates Rab11, and TRAPPIII activates Rab1, with the two complexes sharing a ...The TRAPP complexes are nucleotide exchange factors that play essential roles in membrane traffic and autophagy. TRAPPII activates Rab11, and TRAPPIII activates Rab1, with the two complexes sharing a core of small subunits that affect nucleotide exchange but being distinguished by specific large subunits that are essential for activity in vivo. Crystal structures of core subunits have revealed the mechanism of Rab activation, but how the core and the large subunits assemble to form the complexes is unknown. We report a cryo-EM structure of the entire Drosophila TRAPPIII complex. The TRAPPIII-specific subunits TRAPPC8 and TRAPPC11 hold the catalytic core like a pair of tongs, with TRAPPC12 and TRAPPC13 positioned at the joint between them. TRAPPC2 and TRAPPC2L link the core to the two large arms, with the interfaces containing residues affected by disease-causing mutations. The TRAPPC8 arm is positioned such that it would contact Rab1 that is bound to the core, indicating how the arm could determine the specificity of the complex. A lower resolution structure of TRAPPII shows a similar architecture and suggests that the TRAPP complexes evolved from a single ur-TRAPP.
History
DepositionDec 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 2.0Jun 23, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.label_seq_id / _citation.journal_volume ..._atom_site.label_seq_id / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 2.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

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  • Deposited structure unit
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Assembly

Deposited unit
A: Trafficking protein particle complex subunit
B: GEO08327p1
C: Trafficking protein particle complex subunit
D: Trafficking protein particle complex subunit
E: Probable trafficking protein particle complex subunit 2
F: Trafficking protein particle complex subunit 5
G: Trafficking protein particle complex subunit
H: TRAPPC2L
I: FI18195p1
J: Trafficking protein particle complex subunit 11


Theoretical massNumber of molelcules
Total (without water)265,08810
Polymers265,08810
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area22700 Å2
ΔGint-138 kcal/mol
Surface area96200 Å2
MethodPISA

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Components

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Trafficking protein particle complex ... , 5 types, 6 molecules AGCDFJ

#1: Protein Trafficking protein particle complex subunit


Mass: 20492.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Bet3, BET3, Bet3p, dBet3, Dmel\CG3911, TRAPPC3, CG3911, Dmel_CG3911
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q9VSY8
#3: Protein Trafficking protein particle complex subunit


Mass: 16990.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Bet5, BET5, Bet5p, CG1359-RA, Dmel\CG1359, TRAPPC1, CG1359, Dmel_CG1359
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q9VA95
#4: Protein Trafficking protein particle complex subunit


Mass: 24736.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Trs23, CG9298-RA, Dmel\CG9298, TRAPPC4, TRS23, Trs23p, CG9298, Dmel_CG9298
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q9VLI9
#6: Protein Trafficking protein particle complex subunit 5


Mass: 22371.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Trs31, Dmel\CG10153, TRAPPC5, Trs31p, CG10153, Dmel_CG10153
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q7K2Q8
#9: Protein Trafficking protein particle complex subunit 11


Mass: 81847.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: gry, Dmel\CG17569, gryz, l(3)63Bd, TRAPPC11, CG17569, Dmel_CG17569
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q8IRE3

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Protein , 4 types, 4 molecules BEHI

#2: Protein GEO08327p1 / RH37427p / TRAPP subunit 33


Mass: 17597.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Trs33, BcDNA:RH37427, Dmel\CG6196, dTrs33, TRAPPC6, Trs33p, CG6196, Dmel_CG6196
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q9VF82
#5: Protein Probable trafficking protein particle complex subunit 2 / TRAPP subunit 20 ortholog


Mass: 16669.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Trs20, l(3)72Dh, CG5161
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q9VUZ1
#7: Protein TRAPPC2L


Mass: 15511.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dmel\CG9067, Tca17, TRAPPC2L, CG9067, Dmel_CG9067
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: A1Z8I0
#8: Protein FI18195p1 / Lethal (3) 76BDm / isoform A / isoform B


Mass: 28378.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: l(3)76BDm, Dmel\CG8793, l(3)76BDm-RA, l(3)L3809, TRAPPC8, CG8793, Dmel_CG8793
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q9VW22

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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: MiniTRAPPIII: TRAPPIII complex without the C12 and C13 specific subunits
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.453 MDa / Experimental value: YES
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameBuffer-ID
150 mMHepes-KOH1
2250 mMKAc1
31 mMDTT1
40.005 (v/v)%Igepal C-6301
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 285.15 K

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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 FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.3 sec. / Electron dose: 45.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3443
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
1crYOLO1.5particle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7UCSF Chimera1.5model fitting
8Coot0.9model fitting
11RELION3.1.1final Euler assignment
12RELION3.1.1classification
13RELION3.1.13D reconstruction
14Coot0.9model refinement
15PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1242082
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 486758 / Symmetry type: POINT

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