[English] 日本語
Yorodumi
- PDB-7t7x: Munc13-1 C1-C2B-MUN-C2C Upright conformation spanning two lipid b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7t7x
TitleMunc13-1 C1-C2B-MUN-C2C Upright conformation spanning two lipid bilayers
ComponentsProtein unc-13 homolog A
KeywordsEXOCYTOSIS / Synaptic Transmission / Munc13 / Membrane Fusion
Function / homology
Function and homology information


dense core granule priming / neuronal dense core vesicle exocytosis / diacylglycerol binding / synaptic vesicle maturation / synaptic vesicle docking / regulation of synaptic vesicle priming / positive regulation of synaptic plasticity / positive regulation of dendrite extension / positive regulation of glutamate receptor signaling pathway / regulation of short-term neuronal synaptic plasticity ...dense core granule priming / neuronal dense core vesicle exocytosis / diacylglycerol binding / synaptic vesicle maturation / synaptic vesicle docking / regulation of synaptic vesicle priming / positive regulation of synaptic plasticity / positive regulation of dendrite extension / positive regulation of glutamate receptor signaling pathway / regulation of short-term neuronal synaptic plasticity / neurotransmitter secretion / innervation / regulation of amyloid precursor protein catabolic process / syntaxin binding / presynaptic active zone / syntaxin-1 binding / Golgi-associated vesicle / spectrin binding / positive regulation of neurotransmitter secretion / neuromuscular junction development / synaptic vesicle priming / excitatory synapse / synaptic vesicle exocytosis / amyloid-beta metabolic process / synaptic membrane / calyx of Held / SNARE binding / synaptic transmission, glutamatergic / neuromuscular junction / phospholipid binding / long-term synaptic potentiation / terminal bouton / synaptic vesicle membrane / presynapse / presynaptic membrane / cell differentiation / calmodulin binding / neuron projection / protein domain specific binding / axon / calcium ion binding / synapse / protein-containing complex binding / glutamatergic synapse / protein-containing complex / zinc ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Protein Unc-13 / Protein Unc-13, C2B domain / Mammalian uncoordinated homology 13, domain 2 / Munc13-homology domain 2 (MHD2) profile. / Domain of Unknown Function (DUF1041) / MUN domain / Munc13 homology 1 / MUN domain / Munc13-homology domain 1 (MHD1) profile. / Phorbol esters/diacylglycerol binding domain (C1 domain) ...Protein Unc-13 / Protein Unc-13, C2B domain / Mammalian uncoordinated homology 13, domain 2 / Munc13-homology domain 2 (MHD2) profile. / Domain of Unknown Function (DUF1041) / MUN domain / Munc13 homology 1 / MUN domain / Munc13-homology domain 1 (MHD1) profile. / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Protein kinase C conserved region 2 (CalB) / C2 domain / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C2 domain / C2 domain profile. / C1-like domain superfamily / C2 domain superfamily
Similarity search - Domain/homology
Protein unc-13 homolog A / Protein unc-13 homolog A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 10 Å
AuthorsGrushin, K. / Sindelar, C.V.
Funding support United States, 2items
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 General Medical Sciences (NIH/NIGMS)NIH GM 110530 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Munc13 structural transitions and oligomers that may choreograph successive stages in vesicle priming for neurotransmitter release.
Authors: Kirill Grushin / R Venkat Kalyana Sundaram / Charles V Sindelar / James E Rothman /
Abstract: How can exactly six SNARE complexes be assembled under each synaptic vesicle? Here we report cryo-EM crystal structures of the core domain of Munc13, the key chaperone that initiates SNAREpin ...How can exactly six SNARE complexes be assembled under each synaptic vesicle? Here we report cryo-EM crystal structures of the core domain of Munc13, the key chaperone that initiates SNAREpin assembly. The functional core of Munc13, consisting of C1-C2B-MUN-C2C (Munc13C) spontaneously crystallizes between phosphatidylserine-rich bilayers in two distinct conformations, each in a radically different oligomeric state. In the open conformation (state 1), Munc13C forms upright trimers that link the two bilayers, separating them by ∼21 nm. In the closed conformation, six copies of Munc13C interact to form a lateral hexamer elevated ∼14 nm above the bilayer. Open and closed conformations differ only by a rigid body rotation around a flexible hinge, which when performed cooperatively assembles Munc13 into a lateral hexamer (state 2) in which the key SNARE assembly-activating site of Munc13 is autoinhibited by its neighbor. We propose that each Munc13 in the lateral hexamer ultimately assembles a single SNAREpin, explaining how only and exactly six SNARE complexes are templated. We suggest that state 1 and state 2 may represent two successive states in the synaptic vesicle supply chain leading to "primed" ready-release vesicles in which SNAREpins are clamped and ready to release (state 3).
History
DepositionDec 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-25740
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein unc-13 homolog A


Theoretical massNumber of molelcules
Total (without water)130,8961
Polymers130,8961
Non-polymers00
Water00
1


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

-
Components

#1: Protein Protein unc-13 homolog A / Munc13-1


Mass: 130895.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Unc13a, Unc13h1, Unc13a / Variant: NM_022861 / Cell line (production host): ExpiHEK-293 / Production host: Homo sapiens (human) / References: UniProt: Q62768, UniProt: Q4KUS2

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: subtomogram averaging

-
Sample preparation

ComponentName: 2D crystal of Munc13-1 C1-C2B-MUN-C2C domains between two lipid bilayers.
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.13 MDa / Experimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human) / Cell: ExpiHEK-293
Buffer solutionpH: 7.4
Buffer component
IDConc.NameBuffer-ID
120 mMMOPS1
2150 mMpotassium chloride1
31 mMEDTA1
40.5 mMTCEP1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K / Details: blot for 5 sec before plunging, blot force -1

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 3500 nm
Image recordingElectron dose: 3.1 e/Å2 / Avg electron dose per subtomogram: 110 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV

-
Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
7ISOLDE1.2.0model fitting
8UCSF ChimeraX1.2model fitting
9UCSF Chimera1.16model fitting
13RELION3.1final Euler assignment
15RELION3.13D reconstruction
CTF correctionDetails: CTF correction was performed during 3D reconstruction in RELION 3.1
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 10 Å / Resolution method: OTHER / Num. of particles: 126711
Details: Combined map of best classes from two independent 3D classifications in RELION 3.1 of selected regions without angular searches using C3 symmetry expanded dataset (126711 subtomograms) and ...Details: Combined map of best classes from two independent 3D classifications in RELION 3.1 of selected regions without angular searches using C3 symmetry expanded dataset (126711 subtomograms) and separation into 8 classes.
Symmetry type: POINT
EM volume selectionDetails: Particles were extracted and refined using Warp/M software
Num. of tomograms: 62 / Num. of volumes extracted: 70467
Atomic model buildingProtocol: FLEXIBLE FIT
Details: Model for fitting was generated by AlphaFold using the construct's amino acid sequence. Flexible fitting into 3D map densities was performed using ISOLDE tool in ChimeraX.

+
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