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- PDB-7t81: Model of Munc13-1 C1-C2B-MUN-C2C 2D crystal between lipid bilayers. -

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Basic information

Entry
Database: PDB / ID: 7t81
TitleModel of Munc13-1 C1-C2B-MUN-C2C 2D crystal between 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 / positive regulation of neurotransmitter secretion / spectrin binding / neuromuscular junction development / synaptic vesicle priming / synaptic vesicle exocytosis / excitatory synapse / amyloid-beta metabolic process / calyx of Held / synaptic membrane / 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) / Protein kinase C conserved region 2 (CalB) / Zinc finger phorbol-ester/DAG-type signature. / 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

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Structure visualization

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  • Simplified surface model + fitted atomic model
  • EMDB-25741
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  • EMDB-25741
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Assembly

Deposited unit
A: Protein unc-13 homolog A
C: Protein unc-13 homolog A
D: Protein unc-13 homolog A
E: Protein unc-13 homolog A
F: Protein unc-13 homolog A
G: Protein unc-13 homolog A
H: Protein unc-13 homolog A
I: Protein unc-13 homolog A
J: Protein unc-13 homolog A
K: Protein unc-13 homolog A
L: Protein unc-13 homolog A
M: Protein unc-13 homolog A
N: Protein unc-13 homolog A
O: Protein unc-13 homolog A
P: Protein unc-13 homolog A
Q: Protein unc-13 homolog A
R: Protein unc-13 homolog A
S: Protein unc-13 homolog A
T: Protein unc-13 homolog A
U: Protein unc-13 homolog A
V: Protein unc-13 homolog A
W: Protein unc-13 homolog A
X: Protein unc-13 homolog A
Y: Protein unc-13 homolog A


Theoretical massNumber of molelcules
Total (without water)3,141,50124
Polymers3,141,50124
Non-polymers00
Water00
1


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

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Components

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


Mass: 130895.867 Da / Num. of mol.: 24
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

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Experimental details

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Experiment

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

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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

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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

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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 correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 10 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7
Details: A composite 3D map of the crystal, generated by merging of hexagon-focused and six trimer-focused 3D maps (EMD-25737 and EMD-25738, respectively) in UCSF Chimera using the vop maximum command.
Symmetry type: POINT
EM volume selectionNum. of tomograms: 62 / Num. of volumes extracted: 105070
Atomic model buildingProtocol: FLEXIBLE FIT
Details: Model for fitting was generated by AlphaFold using the construct's amino acid sequence. Flexible fitting into corresponding densities was performed using ISOLDE tool in ChimeraX. The ...Details: Model for fitting was generated by AlphaFold using the construct's amino acid sequence. Flexible fitting into corresponding densities was performed using ISOLDE tool in ChimeraX. The resulting structures were copied and fitted as rigid bodies into the 3D map by the "fit in map" function in Chimera.

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