[English] 日本語
Yorodumi
- PDB-8dit: Cryo-EM structure of a HOPS core complex containing Vps33, Vps16,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dit
TitleCryo-EM structure of a HOPS core complex containing Vps33, Vps16, and Vps18
Components
  • Vacuolar protein sorting-associated protein 16
  • Vacuolar protein sorting-associated protein 18
  • Vacuolar protein sorting-associated protein 33
KeywordsPROTEIN TRANSPORT / HOPS / membrane tethering / SNAREs / membrane fusion / endolysosomal trafficking
Biological speciesChaetomium thermophilum (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.1 Å
AuthorsPort, S.A. / Farrell, P.D. / Jeffrey, P.D. / DiMaio, F. / Hughson, F.M.
Funding support Germany, United States, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)PO2195/1-1 Germany
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071574 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM123089 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of the HOPS core complex and its implication for SNARE assembly
Authors: Port, S.A. / Farrell, P.D. / Jeffrey, P.D. / DiMaio, F. / Hughson, F.M.
History
DepositionJun 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 33
B: Vacuolar protein sorting-associated protein 16
C: Vacuolar protein sorting-associated protein 18


Theoretical massNumber of molelcules
Total (without water)279,8523
Polymers279,8523
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, 1:1:1 stoichiometry
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Vacuolar protein sorting-associated protein 33


Mass: 77119.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Plasmid: pQLinkH-Vps33:Vps16 / Details (production host): co-expression plasmid / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon+
#2: Protein Vacuolar protein sorting-associated protein 16


Mass: 94204.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Plasmid: pQLinkH-Vps33:Vps16 / Details (production host): co-expression plasmid / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon+
#3: Protein Vacuolar protein sorting-associated protein 18


Mass: 108527.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Plasmid: pQLinkN-Vps18 / Production host: Escherichia coli (E. coli) / Variant (production host): C43

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1HOPS core complexCOMPLEXall0RECOMBINANT
2His-Vps33:Vps16COMPLEX#1-#21RECOMBINANT
3Vps18COMPLEX#31RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.280 MDaNO
210.171 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Chaetomium thermophilum (fungus)209285
32Chaetomium thermophilum (fungus)209285
43Chaetomium thermophilum (fungus)209285
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrainPlasmid
21Escherichia coli (E. coli)562
32Escherichia coli (E. coli)562BL21 codon+pQLinkH-Vps33:Vps16
43Escherichia coli (E. coli)562C43 (DE3)pQLinkN-Vps18
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPESHEPES1
2150 mMsodium chlorideNaCl1
31 mMDTTDTT1
SpecimenConc.: 0.08 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: PELCO Easiglow, 10 mA/ 10 s discharge/ 30 s hold / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K
Details: Blotting parameters: 30 seconds waiting time, blotting force 1, blot total 1

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 2000 nm / Cs: 0.03 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5.6 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3590
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 32 / Used frames/image: 1-32

-
Processing

EM software
IDNameVersionCategoryDetails
2EPUimage acquisition
4cryoSPARC2.15.0CTF correction
10cryoSPARC2.15.0initial Euler assignment
11cryoSPARCv2.15.0final Euler assignment
12cryoSPARC2.15.0classification
13cryoSPARC2.15.03D reconstruction
14RELION3.1.03D reconstructionpixel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4092244 / Details: blob picker 60-280A (circular)
3D reconstructionResolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 154917 / Symmetry type: POINT
RefinementHighest resolution: 5.1 Å

+
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