[English] 日本語
Yorodumi
- EMDB-52343: Native intermediate synaptic vesicle tether, likely Munc13 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52343
TitleNative intermediate synaptic vesicle tether, likely Munc13
Map dataIntermediate tether average
Sample
  • Organelle or cellular component: Synaptosome
KeywordsMunc13 Presynaptic Synaptic vesicle tether Active zone complex Synaptic vesicle priming Synaptic transmission / EXOCYTOSIS
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 35.1 Å
AuthorsLucic V / Oroczo-Borunda DH
Funding support France, 1 items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)RGP0020/2019 France
Citation
Journal: To Be Published
Title: Native intermediate synaptic vesicle tether, likely Munc13
Authors: Lucic V / Oroczo-Borunda DH
#1: Journal: To Be Published
Title: Munc13- and SNAP25-dependent molecular bridges play a key role in synaptic vesicle priming. DOI: 10.1126/sciadv.adf6222. PubMed ID: 37343100
Authors: Papantoniou C / Laugks U / Betzin J / Capitanio C / Ferrero JJ / Sanchez-Prieto J / Schoch S / Brose N / Baumeister W / Cooper BH / Imig C / Lucic V
History
DepositionDec 16, 2024-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52343.png

Downloads & links

-
Map

FileDownload / File: emd_52343.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIntermediate tether average
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.78 Å/pix.
x 64 pix.
= 561.92 Å		8.78 Å/pix.
x 64 pix.
= 561.92 Å		8.78 Å/pix.
x 64 pix.
= 561.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.78 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.052
Minimum - Maximum-0.5764185 - 0.64187783
Average (Standard dev.)0.0010648075 (±0.026825009)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 561.92 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Intermediate tether average without vesicle and plasma membrane...

Fileemd_52343_additional_1.map
AnnotationIntermediate tether average without vesicle and plasma membrane contributions
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half 1

Fileemd_52343_half_map_1.map
AnnotationHalf 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half 2

Fileemd_52343_half_map_2.map
AnnotationHalf 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Synaptosome

EntireName: Synaptosome
Components
  • Organelle or cellular component: Synaptosome

-
Supramolecule #1: Synaptosome

SupramoleculeName: Synaptosome / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Synaptosomal fraction from rodent Hippocampus
Source (natural)Organism: Mus musculus (house mouse) / Strain: C57 B6/N / Organ: brain / Tissue: hippocampus / Location in cell: excitatory synapse
Molecular weightTheoretical: 196 KDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.4 / Component - Concentration: 300.0 mM / Component - Formula: HBM / Component - Name: Hepes-buffered medium
Details: 140 mM NaCl, 5 mM KCl, 5mM NaHCO3, 1.2 mM NaH2PO4-H2O, 1 mM MgCl26-H2O, 10 mM Glucose, 10 mM Hepes, 1.2 mM CaCl2
GridModel: Quantifoil Active R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Details: Portable manual plunger made at Max Planck Institute of Biochemistry.
DetailsSynaptosomal fraction (P2) was obtained from DIV 28-30 hippocampal organotypic slices.

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 35.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number subtomograms used: 441
ExtractionNumber tomograms: 77 / Number images used: 760 / Method: Hierarchical connectivity / Software - details: Pyto 1.10
Details: Automatically detected bridges between synaptic vesicles and plasma membrane by hierarchical connectivity algorithm implemented in Pyto software
CTF correctionType: NONE
Final 3D classificationNumber classes: 1 / Avg.num./class: 441 / Software - details: Pyto 1.10
Details: No 3D classification was done. Instead, before particle extraction, all intermediate tethers (760 in total) detected in tomograms were classified by a feature-based deep neuronal network ...Details: No 3D classification was done. Instead, before particle extraction, all intermediate tethers (760 in total) detected in tomograms were classified by a feature-based deep neuronal network into three classes. The class used for refinement and reconstruction contained 441 particles
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

+
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