[English] 日本語
Yorodumi
- EMDB-71039: Subtomogram average of Munc13-1 C1-C2B-MUN-C2C F1176N/I1215N muta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-71039
TitleSubtomogram average of Munc13-1 C1-C2B-MUN-C2C F1176N/I1215N mutant 2D crystal between lipid bilayers
Map dataLow-resolution 3D reconstruction of Munc13C F1176N/I1215N mutant 2D crystal between lipid membranes.
Sample
  • Complex: 2D crystal of Munc13-1 C1-C2B-MUN-C2C F1176N/I1215N mutant between negatively charged lipid bilayers
KeywordsMunc13-1 / 2D crystal / lipid bilayer / mutant / subtomogram averaging / EXOCYTOSIS
Biological speciesRattus norvegicus (Norway rat)
Methodsubtomogram averaging / cryo EM / Resolution: 36.0 Å
AuthorsGrushin K / Radhakrishnan A
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)NIH DK 027044 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NIH NS 130894 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NIH NS 116747 United States
CitationJournal: Nat Commun / Year: 2025
Title: Two successive oligomeric Munc13 assemblies scaffold vesicle docking and SNARE assembly to support neurotransmitter release.
Authors: Manindra Bera / Kirill Grushin / R Venkat Kalyana Sundaram / Jasmine S Hinzen / Joyce Chen / Atrouli Chatterjee / Abhijith Radhakrishnan / Seong Lee / Murugesh Padmanarayana / Jeff Coleman / ...Authors: Manindra Bera / Kirill Grushin / R Venkat Kalyana Sundaram / Jasmine S Hinzen / Joyce Chen / Atrouli Chatterjee / Abhijith Radhakrishnan / Seong Lee / Murugesh Padmanarayana / Jeff Coleman / Frédéric Pincet / James E Rothman / Jeremy S Dittman /
Abstract: The critical protein Munc13 serves numerous roles in the docking and priming of synaptic vesicles. On the presynaptic plasma membrane, Munc13 is organized into nanoclusters corresponding to release ...The critical protein Munc13 serves numerous roles in the docking and priming of synaptic vesicles. On the presynaptic plasma membrane, Munc13 is organized into nanoclusters corresponding to release sites where synaptic vesicles dock and fuse. However, it is currently not known whether there is any organization of Munc13 monomers within the nanoclusters. Recent work suggests that Munc13 may spontaneously self-organize into homo-oligomers, raising the possibility that synaptic nanoclusters comprise organized assemblies of Munc13. Here we investigate the functional impact of two distinct Munc13 core domain oligomers comprising C1-C2B-MUN-C2C both in vitro and in vivo. Interface mutations that specifically destabilized oligomeric assemblies of Munc13 disrupted vesicle docking, trans-SNARE formation, and Ca-triggered vesicle fusion in vitro and impaired neurotransmitter secretion and motor nervous system function in vivo. We suggest that a sequence of oligomeric Munc13 complexes rapidly couple vesicle docking to vesicle priming via the assembly of a precise number of SNAREs.
History
DepositionJun 4, 2025-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_71039.png

Downloads & links

-
Map

FileDownload / File: emd_71039.map.gz / Format: CCP4 / Size: 432.6 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLow-resolution 3D reconstruction of Munc13C F1176N/I1215N mutant 2D crystal between lipid membranes.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
18.1 Å/pix.
x 48 pix.
= 868.8 Å		18.1 Å/pix.
x 48 pix.
= 868.8 Å		18.1 Å/pix.
x 48 pix.
= 868.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 18.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.355
Minimum - Maximum-2.1659951 - 2.3826914
Average (Standard dev.)-0.0013073423 (±0.2582373)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions484848
Spacing484848
CellA=B=C: 868.80005 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map #2 of 3D reconstruction of Munc13C...

Fileemd_71039_half_map_1.map
AnnotationHalf map #2 of 3D reconstruction of Munc13C F1176N/I1215N mutant 2D crystal
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map #1 of 3D reconstruction of Munc13C...

Fileemd_71039_half_map_2.map
AnnotationHalf map #1 of 3D reconstruction of Munc13C F1176N/I1215N mutant 2D crystal
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : 2D crystal of Munc13-1 C1-C2B-MUN-C2C F1176N/I1215N mutant betwee...

EntireName: 2D crystal of Munc13-1 C1-C2B-MUN-C2C F1176N/I1215N mutant between negatively charged lipid bilayers
Components
  • Complex: 2D crystal of Munc13-1 C1-C2B-MUN-C2C F1176N/I1215N mutant between negatively charged lipid bilayers

-
Supramolecule #1: 2D crystal of Munc13-1 C1-C2B-MUN-C2C F1176N/I1215N mutant betwee...

SupramoleculeName: 2D crystal of Munc13-1 C1-C2B-MUN-C2C F1176N/I1215N mutant between negatively charged lipid bilayers
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 130 KDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation state2D array

-
Sample preparation

BufferpH: 7.4
Component:
ConcentrationName
20.0 mMMOPS
150.0 mMPotassium chloride
1.0 mMEDTA
0.5 mMTCEP
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 35 sec.
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 13500

+
Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 36.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number subtomograms used: 3035
ExtractionNumber tomograms: 10 / Number images used: 3035 / Software - Name: Warp (ver. 1.0.9)
CTF correctionSoftware - Name: RELION (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationSoftware - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
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://pdbjlvh1.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