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- PDB-7zu0: HOPS tethering complex from yeast -

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Basic information

Entry
Database: PDB / ID: 7zu0
TitleHOPS tethering complex from yeast
Components
  • (Vacuolar protein sorting-associated protein ...) x 3
  • E3 ubiquitin-protein ligase PEP5
  • Vacuolar membrane protein PEP3
  • Vacuolar morphogenesis protein 6
KeywordsCYTOSOLIC PROTEIN / HOPS / tethering complex / lysosome / membrane fusion / Rab GTPase / cryo-EM
Function / homology
Function and homology information


histone catabolic process / organelle fusion / endosomal vesicle fusion / regulation of SNARE complex assembly / CORVET complex / HOPS complex / vesicle tethering / vacuole-mitochondrion membrane contact site / regulation of vacuole fusion, non-autophagic / vacuolar protein processing ...histone catabolic process / organelle fusion / endosomal vesicle fusion / regulation of SNARE complex assembly / CORVET complex / HOPS complex / vesicle tethering / vacuole-mitochondrion membrane contact site / regulation of vacuole fusion, non-autophagic / vacuolar protein processing / vacuole fusion, non-autophagic / vesicle fusion with vacuole / Golgi to endosome transport / Golgi to vacuole transport / cytoplasm to vacuole targeting by the Cvt pathway / vesicle docking / endosome organization / vacuole organization / protein targeting to vacuole / late endosome to vacuole transport / piecemeal microautophagy of the nucleus / fungal-type vacuole / fungal-type vacuole membrane / vesicle docking involved in exocytosis / endosomal transport / lysosome organization / endosome to lysosome 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 / small GTPase binding / autophagy / endocytosis / ubiquitin protein ligase activity / protein transport / late endosome / protein-macromolecule adaptor activity / actin binding / early endosome membrane / endosome / ATP binding / membrane / metal ion binding / cytoplasm / cytosol
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, domain 2 / Sec1-like, domain 3a / Sec1-like protein / Sec1-like superfamily / 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 / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsShvarev, D. / Schoppe, J. / Koenig, C. / Perz, A. / Fuellbrunn, N. / Kiontke, S. / Langemeyer, L. / Januliene, D. / Schnelle, K. / Kuemmel, D. ...Shvarev, D. / Schoppe, J. / Koenig, C. / Perz, A. / Fuellbrunn, N. / Kiontke, S. / Langemeyer, L. / Januliene, D. / Schnelle, K. / Kuemmel, D. / Froehlich, F. / Moeller, A. / Ungermann, C.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 944 Germany
German Research Foundation (DFG)INST190/196-1 FUGG Germany
German Federal Ministry for Education and ResearchDLR 01ED2010 Germany
CitationJournal: Elife / Year: 2022
Title: Structure of the HOPS tethering complex, a lysosomal membrane fusion machinery.
Authors: Dmitry Shvarev / Jannis Schoppe / Caroline König / Angela Perz / Nadia Füllbrunn / Stephan Kiontke / Lars Langemeyer / Dovile Januliene / Kilian Schnelle / Daniel Kümmel / Florian ...Authors: Dmitry Shvarev / Jannis Schoppe / Caroline König / Angela Perz / Nadia Füllbrunn / Stephan Kiontke / Lars Langemeyer / Dovile Januliene / Kilian Schnelle / Daniel Kümmel / Florian Fröhlich / Arne Moeller / Christian Ungermann /
Abstract: Lysosomes are essential for cellular recycling, nutrient signaling, autophagy, and pathogenic bacteria and viruses invasion. Lysosomal fusion is fundamental to cell survival and requires HOPS, a ...Lysosomes are essential for cellular recycling, nutrient signaling, autophagy, and pathogenic bacteria and viruses invasion. Lysosomal fusion is fundamental to cell survival and requires HOPS, a conserved heterohexameric tethering complex. On the membranes to be fused, HOPS binds small membrane-associated GTPases and assembles SNAREs for fusion, but how the complex fulfills its function remained speculative. Here, we used cryo-electron microscopy to reveal the structure of HOPS. Unlike previously reported, significant flexibility of HOPS is confined to its extremities, where GTPase binding occurs. The SNARE-binding module is firmly attached to the core, therefore, ideally positioned between the membranes to catalyze fusion. Our data suggest a model for how HOPS fulfills its dual functionality of tethering and fusion and indicate why it is an essential part of the membrane fusion machinery.
History
DepositionMay 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_src_gen.gene_src_strain ..._entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession
Revision 1.2Oct 12, 2022Group: Database references / Category: pdbx_database_related

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase PEP5
B: Vacuolar protein sorting-associated protein 16
C: Vacuolar membrane protein PEP3
D: Vacuolar protein sorting-associated protein 33
E: Vacuolar morphogenesis protein 6
F: Vacuolar protein sorting-associated protein 41


Theoretical massNumber of molelcules
Total (without water)636,9406
Polymers636,9406
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, electron microscopy, assay for oligomerization, Mass photometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 3 molecules ACE

#1: Protein E3 ubiquitin-protein ligase PEP5 / Carboxypeptidase Y-deficient protein 5 / Histone E3 ligase PEP5 / RING-type E3 ubiquitin ...Carboxypeptidase Y-deficient protein 5 / Histone E3 ligase PEP5 / RING-type E3 ubiquitin transferase PEP5 / Vacuolar biogenesis protein END1 / Vacuolar morphogenesis protein 1 / Vacuolar protein sorting-associated protein 11 / Vacuolar protein-targeting protein 11


Mass: 117617.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c
Gene: PEP5, END1, VAM1, VPL9, VPS11, VPT11, YMR231W, YM9959.13
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P12868, RING-type E3 ubiquitin transferase
#3: Protein Vacuolar membrane protein PEP3 / Carboxypeptidase Y-deficient protein 3 / Vacuolar morphogenesis protein 8 / Vacuolar protein ...Carboxypeptidase Y-deficient protein 3 / Vacuolar morphogenesis protein 8 / Vacuolar protein sorting-associated protein 18 / Vacuolar protein-targeting protein 18


Mass: 107531.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PEP3, VAM8, VPS18, VPT18, YLR148W, L9634.2 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P27801
#5: Protein Vacuolar morphogenesis protein 6 / Vacuolar protein sorting-associated protein 39


Mass: 123049.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: VAM6, CVT4, VPL18, VPL22, VPS39, YDL077C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q07468

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Vacuolar protein sorting-associated protein ... , 3 types, 3 molecules BDF

#2: Protein Vacuolar protein sorting-associated protein 16 / Vacuolar morphogenesis protein 9 / Vacuolar protein-targeting protein 16


Mass: 92857.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: VPS16, VAM9, VPT16, YPL045W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03308
#4: Protein Vacuolar protein sorting-associated protein 33 / Protein SLP1 / Vacuolar morphogenesis protein 5


Mass: 79354.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: VPS33, SLP1, VAM5, YLR396C, L8084.15 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20795
#6: Protein Vacuolar protein sorting-associated protein 41 / Vacuolar morphogenesis protein 2


Mass: 116530.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: VPS41, FET2, VAM2, YDR080W, D446, YD8554.13 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38959

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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: Tethering complex HOPS / 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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.3.1particle selection
4cryoSPARC3.3.1CTF correction
10cryoSPARC3.3.1initial Euler assignment
11cryoSPARC3.3.1final Euler assignment
12cryoSPARC3.3.1classification
CTF correctionType: NONE
3D reconstructionResolution: 4.4 Å / Resolution method: OTHER / Num. of particles: 244661
Details: Resolution of the consensus map of the lower part of the complex is used here
Symmetry type: POINT

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