[English] 日本語
Yorodumi
- PDB-7zu0: HOPS tethering complex from yeast -

+
Open data


ID or keywords:

Loading...

-
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 / CORVET complex / regulation of SNARE complex assembly / HOPS complex / 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 / regulation of SNARE complex assembly / HOPS complex / endosomal vesicle fusion / vesicle tethering / regulation of vacuole fusion, non-autophagic / vacuole-mitochondrion membrane contact site / vacuolar protein processing / Golgi to vacuole transport / vacuole fusion, non-autophagic / Golgi to endosome transport / vesicle fusion with vacuole / cytoplasm to vacuole targeting by the Cvt pathway / vesicle docking / endosome organization / vacuole organization / protein targeting to vacuole / 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 / guanyl-nucleotide exchange factor activity / cellular response to starvation / intracellular protein transport / macroautophagy / RING-type E3 ubiquitin transferase / small GTPase binding / autophagy / endocytosis / ubiquitin protein ligase activity / late endosome / protein transport / actin binding / early endosome membrane / protein-macromolecule adaptor activity / endosome / zinc ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Vacuolar protein sorting-associated protein 41 / Vps42 beta-propeller / Vps41 TPR-like region / 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 / Vps42 beta-propeller / Vps41 TPR-like region / 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 / PEP5/VPS11 N-terminal / PEP5/VPS11 TPR / 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 / 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
Citation
Journal: 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.
#1: Journal: Nat Commun / Year: 2024
Title: Structure of the endosomal CORVET tethering complex.
Authors: Dmitry Shvarev / Caroline König / Nicole Susan / Lars Langemeyer / Stefan Walter / Angela Perz / Florian Fröhlich / Christian Ungermann / Arne Moeller /
Abstract: Cells depend on their endolysosomal system for nutrient uptake and downregulation of plasma membrane proteins. These processes rely on endosomal maturation, which requires multiple membrane fusion ...Cells depend on their endolysosomal system for nutrient uptake and downregulation of plasma membrane proteins. These processes rely on endosomal maturation, which requires multiple membrane fusion steps. Early endosome fusion is promoted by the Rab5 GTPase and its effector, the hexameric CORVET tethering complex, which is homologous to the lysosomal HOPS. How these related complexes recognize their specific target membranes remains entirely elusive. Here, we solve the structure of CORVET by cryo-electron microscopy and revealed its minimal requirements for membrane tethering. As expected, the core of CORVET and HOPS resembles each other. However, the function-defining subunits show marked structural differences. Notably, we discover that unlike HOPS, CORVET depends not only on Rab5 but also on phosphatidylinositol-3-phosphate (PI3P) and membrane lipid packing defects for tethering, implying that an organelle-specific membrane code enables fusion. Our data suggest that both shape and membrane interactions of CORVET and HOPS are conserved in metazoans, thus providing a paradigm how tethering complexes function.
#2: Journal: 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
Revision 1.3Jul 24, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / em_admin
Item: _em_admin.last_update
Revision 1.4Apr 16, 2025Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Details

Has protein modificationN

-
Experimental details

-
Experiment

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

-
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

-
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more