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Yorodumi- EMDB-25741: A composite 3D map of Munc13-1 C1-C2B-MUN-C2C 2D crystal between ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25741 | |||||||||
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Title | A composite 3D map of Munc13-1 C1-C2B-MUN-C2C 2D crystal between lipid bilayers. | |||||||||
Map data | Composite 2D crystal map | |||||||||
Sample |
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Keywords | Synaptic Transmission / Munc13 / Membrane Fusion / EXOCYTOSIS | |||||||||
Function / homology | Function and homology information dense core granule priming / neuronal dense core vesicle exocytosis / diacylglycerol binding / presynaptic dense core vesicle exocytosis / synaptic vesicle docking / regulation of synaptic vesicle priming / synaptic vesicle maturation / positive regulation of glutamate receptor signaling pathway / presynaptic active zone cytoplasmic component / positive regulation of synaptic plasticity ...dense core granule priming / neuronal dense core vesicle exocytosis / diacylglycerol binding / presynaptic dense core vesicle exocytosis / synaptic vesicle docking / regulation of synaptic vesicle priming / synaptic vesicle maturation / positive regulation of glutamate receptor signaling pathway / presynaptic active zone cytoplasmic component / positive regulation of synaptic plasticity / innervation / positive regulation of dendrite extension / neurotransmitter secretion / regulation of short-term neuronal synaptic plasticity / regulation of amyloid precursor protein catabolic process / syntaxin binding / syntaxin-1 binding / positive regulation of neurotransmitter secretion / synaptic vesicle priming / Golgi-associated vesicle / neuromuscular junction development / spectrin binding / presynaptic active zone / synaptic vesicle exocytosis / excitatory synapse / calyx of Held / amyloid-beta metabolic process / SNARE binding / synaptic membrane / synaptic transmission, glutamatergic / long-term synaptic potentiation / neuromuscular junction / terminal bouton / phospholipid binding / synaptic vesicle membrane / presynapse / presynaptic membrane / cell differentiation / calmodulin binding / neuron projection / protein domain specific binding / axon / glutamatergic synapse / calcium ion binding / synapse / protein-containing complex binding / protein-containing complex / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 10.0 Å | |||||||||
Authors | Grushin K / Sindelar CV | |||||||||
Funding support | United States, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_25741.map.gz | 53.6 MB | EMDB map data format | |
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Header (meta data) | emd-25741-v30.xml emd-25741.xml | 13.9 KB 13.9 KB | Display Display | EMDB header |
Images | emd_25741.png | 116.7 KB | ||
Filedesc metadata | emd-25741.cif.gz | 6.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25741 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25741 | HTTPS FTP |
-Validation report
Summary document | emd_25741_validation.pdf.gz | 505.6 KB | Display | EMDB validaton report |
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Full document | emd_25741_full_validation.pdf.gz | 505.2 KB | Display | |
Data in XML | emd_25741_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | emd_25741_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25741 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25741 | HTTPS FTP |
-Related structure data
Related structure data | 7t81MC 7t7cC 7t7rC 7t7vC 7t7xC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_25741.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Composite 2D crystal map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : 2D crystal of Munc13-1 C1-C2B-MUN-C2C domains between two lipid b...
Entire | Name: 2D crystal of Munc13-1 C1-C2B-MUN-C2C domains between two lipid bilayers. |
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Components |
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-Supramolecule #1: 2D crystal of Munc13-1 C1-C2B-MUN-C2C domains between two lipid b...
Supramolecule | Name: 2D crystal of Munc13-1 C1-C2B-MUN-C2C domains between two lipid bilayers. type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 130 KDa |
-Macromolecule #1: Protein unc-13 homolog A
Macromolecule | Name: Protein unc-13 homolog A / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 130.895867 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GPLGSEFMAG ITSALASSTL NNEELKNHVY KKTLQALIYP ISCTTPHNFE VWTATTPTYC YECEGLLWGI ARQGMRCTEC GVKCHEKCQ DLLNADCLQR AAEKSSKHGA EDRTQNIIMV LKDRMKIRER NKPEIFELIQ EVFAVTKSAH TQQMKAVKQS V LDGTSKWS ...String: GPLGSEFMAG ITSALASSTL NNEELKNHVY KKTLQALIYP ISCTTPHNFE VWTATTPTYC YECEGLLWGI ARQGMRCTEC GVKCHEKCQ DLLNADCLQR AAEKSSKHGA EDRTQNIIMV LKDRMKIRER NKPEIFELIQ EVFAVTKSAH TQQMKAVKQS V LDGTSKWS AKISITVVCA QGLQAKDKTG SSDPYVTVQV GKTKKRTKTI YGNLNPVWEE NFHFECHNSS DRIKVRVWDE DD DIKSRVK QRFKRESDDF LGQTIIEVRT LSGEMDVWYN LDKRTDKSAV SGAIRLHISV EIKGEEKVAP YHVQYTCLHE NLF HFVTDV QNNGVVKIPD AKGDDAWKVY YDETAQEIVD EFAMRYGVES IYQAMTHFAC LSSKYMCPGV PAVMSTLLAN INAY YAHTT ASTNVSASDR FAASNFGKER FVKLLDQLHN SLRIDLSMYR NNFPASSPER LQDLKSTVDL LTSITFFRMK VQELQ SPPR ASQVVKDCVK ACLNSTYEYI FNNCHELYGR EYQTDPAKKG EVPPEEQGPS IKNLDFWSKL ITLIVSIIEE DKNSYT PCL NQFPQELNVG KISAEVMWSL FAQDMKYAME EHDKHRLCKS ADYMNLHFKV KWLYNEYVAE LPTFKDRVPE YPAWFEP FV IQWLDENEEV SRDFLHGALE RDKKDGFQQT SEHALFSCSV VDVFSQLNQS FEIIKKLECP DPQIVGHYMR RFAKTISN V LLQYADIVSK DFASYCSKEK EKVPCILMNN TQQLRVQLEK MFEAMGGKEL DAEASGTLKE LQVKLNNVLD ELSHVFATS FQPHIEECVR QMGDILSQVK GTGNVPASAC SSVAQDADNV LQPIMDLLDS NLTLFAKICE KTVLKRVLKE LWKLVMNTME RTIVLPPEF LSKLKDHMVR EEAKSLTPKQ CAVVELALDT IKQYFHAGGV GLKKTFLEKS PDLQSLRYAL SLYTQATDLL I KTFVQTQS AQGSGVEDPV GEVSVHVELF THPGTGEQKV TVKVVAANDL KWQTSGIFRP FIEVNIVGPQ LSDKKRKFAT KS KNNSWAP KYNESFQFSL SADAGPECYE LQVCVKDYCF AREDRTVGLA VLQLRELAQR GSAACWLPLG RRIHMDDTGL TVL RILSQR SNDEVAKEFV KLKSDTRSAE EGGAAPAP UniProtKB: Protein unc-13 homolog A, Protein unc-13 homolog A |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | 2D array |
-Sample preparation
Buffer | pH: 7.4 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 5 sec before plunging, blot force -1. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) 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. Number subtomograms used: 7 |
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Extraction | Number tomograms: 62 / Number images used: 105070 |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) |
-Atomic model buiding 1
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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Refinement | Protocol: FLEXIBLE FIT |
Output model | PDB-7t81: |