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- EMDB-5214: Molecular architecture of the yeast TRAPPII tethering complex - form2 -

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Basic information

Entry
Database: EMDB / ID: EMD-5214
TitleMolecular architecture of the yeast TRAPPII tethering complex - form2
Map dataThis is an image of a surface rendered top-view of TRAPPII form2
Sample
  • Sample: Yeast TRAPPII complex
  • Protein or peptide: Bet3
  • Protein or peptide: Bet5
  • Protein or peptide: Trs20
  • Protein or peptide: Trs23
  • Protein or peptide: Trs31
  • Protein or peptide: Trs33
  • Protein or peptide: Kre11
  • Protein or peptide: Trs120
  • Protein or peptide: Trs130
Keywordstethering complex / guanine nucleotide exchange factor
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 34.0 Å
AuthorsYip CK / Berscheminski J / Walz T
CitationJournal: Nat Struct Mol Biol / Year: 2010
Title: Molecular architecture of the TRAPPII complex and implications for vesicle tethering.
Authors: Calvin K Yip / Julia Berscheminski / Thomas Walz /
Abstract: Multisubunit tethering complexes participate in the process of vesicle tethering--the initial interaction between transport vesicles and their acceptor compartments. TRAPPII (named for transport ...Multisubunit tethering complexes participate in the process of vesicle tethering--the initial interaction between transport vesicles and their acceptor compartments. TRAPPII (named for transport protein particle II) is a highly conserved tethering complex that functions in the late Golgi apparatus and consists of all of the subunits of TRAPPI and three additional, specific subunits. We have purified native yeast TRAPPII and characterized its structure and subunit organization by single-particle EM. Our data show that the nine TRAPPII components form a core complex that dimerizes into a three-layered, diamond-shaped structure. The TRAPPI subunits assemble into TRAPPI complexes that form the outer layers. The three TRAPPII-specific subunits cap the ends of TRAPPI and form the middle layer, which is responsible for dimerization. TRAPPII binds the Ypt1 GTPase and probably uses the TRAPPI catalytic core to promote guanine nucleotide exchange. We discuss the implications of the structure of TRAPPII for coat interaction and TRAPPII-associated human pathologies.
History
DepositionJul 16, 2010-
Header (metadata) releaseJul 23, 2010-
Map releaseFeb 7, 2011-
UpdateFeb 7, 2011-
Current statusFeb 7, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.047
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.047
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5214_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5214.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is an image of a surface rendered top-view of TRAPPII form2
Voxel sizeX=Y=Z: 4.2 Å
Density
Contour LevelBy AUTHOR: 0.063 / Movie #1: 0.047
Minimum - Maximum-0.0404056 - 1.03483
Average (Standard dev.)0.00310599 (±0.0323773)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 537.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.24.24.2
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z537.600537.600537.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-99-99-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.0401.0350.003

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Supplemental data

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Sample components

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Entire : Yeast TRAPPII complex

EntireName: Yeast TRAPPII complex
Components
  • Sample: Yeast TRAPPII complex
  • Protein or peptide: Bet3
  • Protein or peptide: Bet5
  • Protein or peptide: Trs20
  • Protein or peptide: Trs23
  • Protein or peptide: Trs31
  • Protein or peptide: Trs33
  • Protein or peptide: Kre11
  • Protein or peptide: Trs120
  • Protein or peptide: Trs130

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Supramolecule #1000: Yeast TRAPPII complex

SupramoleculeName: Yeast TRAPPII complex / type: sample / ID: 1000 / Number unique components: 9
Molecular weightTheoretical: 1.0 MDa

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Macromolecule #1: Bet3

MacromoleculeName: Bet3 / type: protein_or_peptide / ID: 1 / Name.synonym: Bet3 / Number of copies: 4 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: budding yeast
Molecular weightExperimental: 22 KDa / Theoretical: 22 KDa

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Macromolecule #2: Bet5

MacromoleculeName: Bet5 / type: protein_or_peptide / ID: 2 / Name.synonym: Bet5 / Number of copies: 2 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: budding yeast
Molecular weightExperimental: 18 KDa / Theoretical: 18 KDa

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Macromolecule #3: Trs20

MacromoleculeName: Trs20 / type: protein_or_peptide / ID: 3 / Name.synonym: Trs20 / Number of copies: 2 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: budding yeast
Molecular weightExperimental: 20 KDa / Theoretical: 20 KDa

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Macromolecule #4: Trs23

MacromoleculeName: Trs23 / type: protein_or_peptide / ID: 4 / Name.synonym: Trs23 / Number of copies: 2 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: budding yeast
Molecular weightExperimental: 25 KDa / Theoretical: 25 KDa

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Macromolecule #5: Trs31

MacromoleculeName: Trs31 / type: protein_or_peptide / ID: 5 / Name.synonym: Trs31 / Number of copies: 2 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: budding yeast
Molecular weightExperimental: 32 KDa / Theoretical: 32 KDa

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Macromolecule #6: Trs33

MacromoleculeName: Trs33 / type: protein_or_peptide / ID: 6 / Name.synonym: Trs33 / Number of copies: 2 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: budding yeast
Molecular weightExperimental: 31 KDa / Theoretical: 31 KDa

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Macromolecule #7: Kre11

MacromoleculeName: Kre11 / type: protein_or_peptide / ID: 7 / Name.synonym: Kre11 / Number of copies: 2 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: budding yeast
Molecular weightExperimental: 63 KDa / Theoretical: 63 KDa

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Macromolecule #8: Trs120

MacromoleculeName: Trs120 / type: protein_or_peptide / ID: 8 / Name.synonym: Trs120 / Number of copies: 2 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: budding yeast
Molecular weightExperimental: 148 KDa / Theoretical: 148 KDa

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Macromolecule #9: Trs130

MacromoleculeName: Trs130 / type: protein_or_peptide / ID: 9 / Name.synonym: Trs130 / Number of copies: 2 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: budding yeast
Molecular weightExperimental: 128 KDa / Theoretical: 128 KDa

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.005 mg/mL
BufferpH: 8
Details: 10mM Tris-HCl 8.0, 150mM NaCl, 1mM Mg Acetate, 1mM imidazole, 20mM EGTA, 2mM beta-mercaptoethanol, 0.1% CHAPS
StainingType: NEGATIVE
Details: Protein solution was adsorbed onto grids for 60 seconds before staining with 0.75% uranyl formate
GridDetails: 400 mesh Quantifoil R1.2/1.3 overlaid with thin carbon
VitrificationCryogen name: NITROGEN / Chamber temperature: 100 K / Instrument: OTHER / Method: Manual plunging into liquid nitrogen

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureAverage: 100 K
DetailsLow dose imaging, same specimen area imaged twice
DateSep 4, 2009
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 21 µm / Number real images: 208
Tilt angle min0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 51159 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.4 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder.This holder operates in the temperature range from -175 C to ambient, and gives a resolution of at least 0.34 nm
Specimen holder model: OTHER / Tilt angle max: 45
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsThe particles were selected manually.
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 34.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Details: Final map was filtered to 34 Angstroms / Number images used: 1686
Final two d classificationNumber classes: 2

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Atomic model buiding 1

Initial model
PDB IDChain

2j3w

chain_id: A, chain_id: B, chain_id: D

2j3t

chain_id: A, chain_id: B, chain_id: C, chain_id: D
SoftwareName: Chimera
DetailsPDBEntryID_givenInChain. Protocol: Rigid body. The full TRAPPI model was generated based on the two pdb entries listed and a third pdb file 3CUE. This model was manually docked into density map and further refined using Chimera.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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