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- EMDB-2280: Negative stain EM structure of the HOPS tethering complex (confor... -

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Basic information

Entry
Database: EMDB / ID: EMD-2280
TitleNegative stain EM structure of the HOPS tethering complex (conformation 1)
Map dataReconstruction of HOPS tethering complex
Sample
  • Sample: vacuole protein sorting (HOPS) tethering complex containing Vps11, Vps16, Vps18, Vps33, Vp39, Vps41
  • Protein or peptide: vacuolar protein sorting-associated protein 41
  • Protein or peptide: vacuolar protein sorting-associated protein 39
  • Protein or peptide: vacuolar protein sorting-associated protein 33
  • Protein or peptide: vacuolar protein sorting-associated protein 18
  • Protein or peptide: vacuolar protein sorting-associated protein 11
  • Protein or peptide: vacuolar protein sorting-associated protein 16
Keywordsvesicular transport / homotypic fusion / multisubunit tethering complex / Rab binding
Function / homology
Function and homology information


histone catabolic process / organelle fusion / CORVET complex / HOPS complex / regulation of SNARE complex assembly / endosomal vesicle fusion / vesicle tethering / regulation of vacuole fusion, non-autophagic / vacuole-mitochondrion membrane contact site / vacuolar protein processing ...histone catabolic process / organelle fusion / CORVET complex / HOPS complex / regulation of SNARE complex assembly / endosomal vesicle fusion / vesicle tethering / regulation of vacuole fusion, non-autophagic / vacuole-mitochondrion membrane contact site / vacuolar protein processing / vacuole fusion, non-autophagic / vesicle fusion with vacuole / Golgi to endosome transport / cytoplasm to vacuole targeting by the Cvt pathway / Golgi to vacuole transport / vesicle docking / endosome organization / protein targeting to vacuole / vacuole organization / late endosome to vacuole transport / fungal-type vacuole / piecemeal microautophagy of the nucleus / fungal-type vacuole membrane / vesicle docking involved in exocytosis / endosomal transport / vesicle-mediated transport / positive regulation of TORC1 signaling / cellular response to starvation / guanyl-nucleotide exchange factor activity / macroautophagy / intracellular protein transport / RING-type E3 ubiquitin transferase / autophagy / small GTPase binding / endocytosis / ubiquitin protein ligase activity / protein transport / late endosome / actin binding / protein-macromolecule adaptor activity / early endosome membrane / endosome / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Vacuolar protein sorting-associated protein 41 / Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated domain 2 / Vacuolar sorting protein 39 domain 2 / Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated domain 1 / Vacuolar protein sorting-associated protein Vps41/Vps8 / Vacuolar sorting protein 39 domain 1 / Pep3/Vps18/deep orange / Vacuolar protein sorting-associated protein 11 / Vacuolar protein sorting protein 11, C-terminal / Pep3/Vps18/deep orange beta-propeller domain ...Vacuolar protein sorting-associated protein 41 / Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated domain 2 / Vacuolar sorting protein 39 domain 2 / Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated domain 1 / Vacuolar protein sorting-associated protein Vps41/Vps8 / Vacuolar sorting protein 39 domain 1 / Pep3/Vps18/deep orange / Vacuolar protein sorting-associated protein 11 / Vacuolar protein sorting protein 11, C-terminal / Pep3/Vps18/deep orange beta-propeller domain / Vacuolar protein sorting protein 11 C terminal / Vam6/VPS39/TRAP1 family / Vps16, C-terminal / Vps16, N-terminal / Vacuolar protein sorting-associated protein 16 / Vps16, C-terminal domain superfamily / Vps16, C-terminal region / Vps16, N-terminal region / Vacuolar protein sorting-associated protein 33, domain 3b / Sec1-like protein / Sec1-like, domain 2 / Sec1-like superfamily / Sec1-like, domain 3a / Sec1 family / Region in Clathrin and VPS / Clathrin heavy chain repeat homology / Clathrin, heavy chain/VPS, 7-fold repeat / Clathrin heavy-chain (CHCR) repeat profile. / Ring finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase PEP5 / Vacuolar protein sorting-associated protein 33 / Vacuolar membrane protein PEP3 / Vacuolar protein sorting-associated protein 41 / Vacuolar protein sorting-associated protein 16 / Vacuolar morphogenesis protein 6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / negative staining / Resolution: 30.4 Å
AuthorsBroecker C / Kuhlee A / Gatsogiannis C / Balderhaar HJ / Hoenscher C / Engelbrecht-Vandre S / Ungermann C / Raunser S
CitationJournal: Proc Natl Acad Sci U S A / Year: 2012
Title: Molecular architecture of the multisubunit homotypic fusion and vacuole protein sorting (HOPS) tethering complex.
Authors: Cornelia Bröcker / Anne Kuhlee / Christos Gatsogiannis / Henning J kleine Balderhaar / Carina Hönscher / Siegfried Engelbrecht-Vandré / Christian Ungermann / Stefan Raunser /
Abstract: Membrane fusion within the eukaryotic endomembrane system depends on the initial recognition of Rab GTPase on transport vesicles by multisubunit tethering complexes and subsequent coupling to SNARE- ...Membrane fusion within the eukaryotic endomembrane system depends on the initial recognition of Rab GTPase on transport vesicles by multisubunit tethering complexes and subsequent coupling to SNARE-mediated fusion. The conserved vacuolar/lysosomal homotypic fusion and vacuole protein sorting (HOPS) tethering complex combines both activities. Here we present the overall structure of the fusion-active HOPS complex. Our data reveal a flexible ≈30-nm elongated seahorse-like structure, which can adopt contracted and elongated shapes. Surprisingly, both ends of the HOPS complex contain a Rab-binding subunit: Vps41 and Vps39. The large head contains in addition to Vps41 the SNARE-interacting Vps33, whereas Vps39 is found in the bulky tip of its tail. Vps11 and Vps18 connect head and tail. Our data suggest that HOPS bridges Ypt7-positive membranes and chaperones SNAREs at fusion sites.
History
DepositionJan 16, 2013-
Header (metadata) releaseJan 23, 2013-
Map releaseJan 23, 2013-
UpdateJan 23, 2013-
Current statusJan 23, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

2280-image1....

Downloads & links

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Map

FileDownload / File: emd_2280.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of HOPS tethering complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.2 Å/pix.
x 128 pix.
= 537.6 Å		4.2 Å/pix.
x 128 pix.
= 537.6 Å		4.2 Å/pix.
x 128 pix.
= 537.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.02741734 - 0.07474332
Average (Standard dev.)0.0003598 (±0.00357346)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 537.6 Å
α=β=γ: 90.0 °

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-36-30-80
NX/NY/NZ7361161
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.0270.0750.000

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Supplemental data

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Sample components

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Entire : vacuole protein sorting (HOPS) tethering complex containing Vps11...

EntireName: vacuole protein sorting (HOPS) tethering complex containing Vps11, Vps16, Vps18, Vps33, Vp39, Vps41
Components
  • Sample: vacuole protein sorting (HOPS) tethering complex containing Vps11, Vps16, Vps18, Vps33, Vp39, Vps41
  • Protein or peptide: vacuolar protein sorting-associated protein 41
  • Protein or peptide: vacuolar protein sorting-associated protein 39
  • Protein or peptide: vacuolar protein sorting-associated protein 33
  • Protein or peptide: vacuolar protein sorting-associated protein 18
  • Protein or peptide: vacuolar protein sorting-associated protein 11
  • Protein or peptide: vacuolar protein sorting-associated protein 16

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Supramolecule #1000: vacuole protein sorting (HOPS) tethering complex containing Vps11...

SupramoleculeName: vacuole protein sorting (HOPS) tethering complex containing Vps11, Vps16, Vps18, Vps33, Vp39, Vps41
type: sample / ID: 1000 / Details: Vps39 is fused to GFP, Vps41 is fused to TAP-tag / Oligomeric state: Monomer / Number unique components: 6
Molecular weightTheoretical: 700 KDa

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Macromolecule #1: vacuolar protein sorting-associated protein 41

MacromoleculeName: vacuolar protein sorting-associated protein 41 / type: protein_or_peptide / ID: 1 / Name.synonym: FET2, VAM2, vps41 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast
SequenceUniProtKB: Vacuolar protein sorting-associated protein 41 / GO: HOPS complex

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Macromolecule #2: vacuolar protein sorting-associated protein 39

MacromoleculeName: vacuolar protein sorting-associated protein 39 / type: protein_or_peptide / ID: 2 / Name.synonym: VAM6,CVT4, VPL18, VPL22, vps39 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast
SequenceUniProtKB: Vacuolar morphogenesis protein 6 / GO: HOPS complex

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Macromolecule #3: vacuolar protein sorting-associated protein 33

MacromoleculeName: vacuolar protein sorting-associated protein 33 / type: protein_or_peptide / ID: 3
Name.synonym: Protein SLP1, Vacuolar morphogenesis protein 5, vps33
Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast
SequenceUniProtKB: Vacuolar protein sorting-associated protein 33 / GO: HOPS complex

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Macromolecule #4: vacuolar protein sorting-associated protein 18

MacromoleculeName: vacuolar protein sorting-associated protein 18 / type: protein_or_peptide / ID: 4 / Name.synonym: PEP3, VAM8, VPT18, vps18 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast
SequenceUniProtKB: Vacuolar membrane protein PEP3 / GO: HOPS complex

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Macromolecule #5: vacuolar protein sorting-associated protein 11

MacromoleculeName: vacuolar protein sorting-associated protein 11 / type: protein_or_peptide / ID: 5 / Name.synonym: END1, VAM1, VPL9, VPS11, VPT11, YMR231W / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast
SequenceUniProtKB: E3 ubiquitin-protein ligase PEP5 / GO: HOPS complex

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Macromolecule #6: vacuolar protein sorting-associated protein 16

MacromoleculeName: vacuolar protein sorting-associated protein 16 / type: protein_or_peptide / ID: 6 / Name.synonym: VAM9, VPT16 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast
SequenceUniProtKB: Vacuolar protein sorting-associated protein 16 / GO: HOPS complex

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Details: 1 M NaCl, 50 mM Hepes/NaOH, 10% glycerol
StainingType: NEGATIVE
Details: Grids with adsorbed Protein floated on 0.07% Uranyl Formate for 1-3h at 4C.
GridDetails: glow discharged 400 mesh copper grids with thin carbon support
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 1400
DateFeb 7, 2011
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 10.5 µm / Number real images: 920 / Average electron dose: 4.5 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 3.4 mm / Nominal defocus max: 0.0017 µm / Nominal defocus min: 0.0013 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: JEOL

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 30.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPARX / Number images used: 2979

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