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- PDB-6a30: Crystal Structure of Munc13-1 MUN Domain and Synaptobrevin-2 Juxt... -

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Basic information

Entry
Database: PDB / ID: 6a30
TitleCrystal Structure of Munc13-1 MUN Domain and Synaptobrevin-2 Juxtamembrane Linker Region
Components
  • Protein unc-13 homolog A
  • Synaptobrevin-2 juxtamembrane linker peptide
KeywordsEXOCYTOSIS / Synaptic exocytosis / Membrane fusion / Munc13 / Munc18 / SNARE / Synaptobrevin
Function / homology
Function and homology information


dense core granule priming / neuronal dense core vesicle exocytosis / trans-Golgi Network Vesicle Budding / positive regulation of glutamate receptor signaling pathway / regulation of delayed rectifier potassium channel activity / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / diacylglycerol binding / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex ...dense core granule priming / neuronal dense core vesicle exocytosis / trans-Golgi Network Vesicle Budding / positive regulation of glutamate receptor signaling pathway / regulation of delayed rectifier potassium channel activity / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / diacylglycerol binding / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / Lysosome Vesicle Biogenesis / regulation of synaptic vesicle priming / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / zymogen granule membrane / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / regulated exocytosis / Dopamine Neurotransmitter Release Cycle / Golgi Associated Vesicle Biogenesis / presynaptic dense core vesicle exocytosis / storage vacuole / synaptic vesicle docking / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / eosinophil degranulation / vesicle fusion / synaptic vesicle maturation / SNARE complex / Golgi to plasma membrane protein transport / SNAP receptor activity / presynaptic active zone cytoplasmic component / regulation of vesicle-mediated transport / Cargo recognition for clathrin-mediated endocytosis / positive regulation of synaptic plasticity / Clathrin-mediated endocytosis / hormone secretion / calcium-ion regulated exocytosis / innervation / positive regulation of intracellular protein transport / regulation of exocytosis / neurotransmitter secretion / positive regulation of dendrite extension / regulation of short-term neuronal synaptic plasticity / neuron projection terminus / regulation of synaptic vesicle recycling / regulation of amyloid precursor protein catabolic process / syntaxin-1 binding / SNARE complex assembly / positive regulation of neurotransmitter secretion / synaptic vesicle priming / syntaxin binding / clathrin-coated vesicle / Golgi-associated vesicle / spectrin binding / neuromuscular junction development / myosin binding / presynaptic active zone / synaptic vesicle exocytosis / calyx of Held / excitatory synapse / synaptic vesicle endocytosis / response to glucose / amyloid-beta metabolic process / vesicle-mediated transport / SNARE binding / secretory granule / synaptic membrane / synaptic transmission, glutamatergic / long-term synaptic potentiation / establishment of localization in cell / phospholipid binding / neuromuscular junction / cytoplasmic vesicle membrane / trans-Golgi network / terminal bouton / synaptic vesicle membrane / cellular response to insulin stimulus / calcium-dependent protein binding / synaptic vesicle / presynapse / presynaptic membrane / cytoplasmic vesicle / protein-containing complex assembly / vesicle / transmembrane transporter binding / membrane fusion / cell differentiation / molecular adaptor activity / calmodulin binding / axon / protein domain specific binding / synapse / glutamatergic synapse / lipid binding / calcium ion binding / protein-containing complex binding / perinuclear region of cytoplasm / protein-containing complex
Similarity search - Function
Mammalian uncoordinated homology 13, domain 2 / Protein Unc-13 / Protein Unc-13, C2B domain / Munc13-homology domain 2 (MHD2) profile. / MUN domain / Munc13 homology 1 / MUN domain / Munc13-homology domain 1 (MHD1) profile. / Domain of Unknown Function (DUF1041) / Synaptobrevin/Vesicle-associated membrane protein ...Mammalian uncoordinated homology 13, domain 2 / Protein Unc-13 / Protein Unc-13, C2B domain / Munc13-homology domain 2 (MHD2) profile. / MUN domain / Munc13 homology 1 / MUN domain / Munc13-homology domain 1 (MHD1) profile. / Domain of Unknown Function (DUF1041) / Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain / Protein kinase C conserved region 2 (CalB) / 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
Vesicle-associated membrane protein 2 / Protein unc-13 homolog A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.793 Å
AuthorsWang, S. / Li, Y. / Gong, J.H. / Ye, S. / Yang, X.F. / Zhang, R.G. / Ma, C.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670846 China
National Natural Science Foundation of China31670850 China
National Natural Science Foundation of China31721002 China
National Basic Research Program of China (973 Program)2015CB910800 China
CitationJournal: Nat Commun / Year: 2019
Title: Munc18 and Munc13 serve as a functional template to orchestrate neuronal SNARE complex assembly.
Authors: Wang, S. / Li, Y. / Gong, J.H. / Ye, S. / Yang, X.F. / Zhang, R.G. / Ma, C.
History
DepositionJun 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein unc-13 homolog A
P: Synaptobrevin-2 juxtamembrane linker peptide


Theoretical massNumber of molelcules
Total (without water)62,7272
Polymers62,7272
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-5 kcal/mol
Surface area28740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.481, 270.967, 47.915
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 61800.781 Da / Num. of mol.: 1 / Fragment: MUN domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Unc13a, Unc13h1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q62768
#2: Protein/peptide Synaptobrevin-2 juxtamembrane linker peptide / Peptide from Vesicle-associated membrane protein 2


Mass: 926.071 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P63045
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.92 Å3/Da / Density % sol: 79.24 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, magnesium nitrate, 2-(N-Morpholino)ethanesulfonic acid (MES)
PH range: 5.8 - 6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 37919 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rsym value: 0.095 / Net I/σ(I): 24.7
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.666 / Num. unique obs: 1840

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y21

4y21


Resolution: 2.793→42.01 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.65
RfactorNum. reflection% reflection
Rfree0.2387 1900 5.01 %
Rwork0.2073 --
obs0.2089 37919 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 209.31 Å2 / Biso mean: 88.51 Å2 / Biso min: 41.23 Å2
Refinement stepCycle: final / Resolution: 2.793→42.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4328 0 0 19 4347
Biso mean---64.18 -
Num. residues----533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044418
X-RAY DIFFRACTIONf_angle_d0.8835967
X-RAY DIFFRACTIONf_chiral_restr0.062664
X-RAY DIFFRACTIONf_plane_restr0.005761
X-RAY DIFFRACTIONf_dihedral_angle_d16.0541669
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7933-2.86320.30551260.28332431255796
2.8632-2.94060.30731380.256925172655100
2.9406-3.02710.27881180.245325642682100
3.0271-3.12470.28671210.249925372658100
3.1247-3.23640.30131400.267725552695100
3.2364-3.36590.3041380.238625412679100
3.3659-3.5190.28641190.241325492668100
3.519-3.70440.28881250.224426202745100
3.7044-3.93640.24681590.206725502709100
3.9364-4.240.22371390.185825702709100
4.24-4.66620.20321460.16525782724100
4.6662-5.34030.21161400.171126462786100
5.3403-6.72370.26341420.238826382780100
6.7237-42.01520.20271490.19612723287297
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8956-1.18940.52578.378-0.30171.7661-0.0185-0.1016-0.34190.73560.19980.37030.2772-0.0094-0.17940.6565-0.04810.0120.53870.05520.5066111.578614.381213.7376
24.1058-1.1803-1.29632.7988-1.96485.0277-0.0801-0.14670.3389-0.2607-0.035-0.0778-0.13340.08380.27490.6485-0.0212-0.05250.46780.10730.3977112.705135.58739.193
33.0263-2.57750.9695.6565-4.14733.3895-0.048-0.0918-0.12860.03510.21450.7319-0.1751-0.6495-0.17460.6091-0.0278-0.06920.67230.0850.518899.847939.02426.1022
40.9004-3.84212.99967.4427-4.20064.464-0.3093-0.03240.22220.39410.1623-0.0909-0.5072-0.23320.16650.66020.0981-0.12030.76860.13330.728289.907368.56-12.8015
54.3873-3.84333.67124.8642-3.23993.9663-0.3954-0.02430.49750.425-0.2049-0.918-0.30940.53180.43690.65530.0308-0.03920.59170.09040.62774.990490.87-37.4566
62.02220.07450.0093-0.14090.21270.96840.0666-0.3496-0.36690.204-0.07430.0730.22610.12720.0270.65430.04560.01610.69270.18530.601260.606888.3728-36.625
70.05780.0848-0.03760.1236-0.05840.0446-0.6926-0.3990.0071-0.072.3853-1.02060.2059-1.00270.26921.47240.3885-0.12241.84310.05161.171385.729282.1249-43.5302
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 944 through 1035 )A944 - 1035
2X-RAY DIFFRACTION2chain 'A' and (resid 1036 through 1085 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1086 through 1165 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1166 through 1325 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1326 through 1405 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1406 through 1480 )A0
7X-RAY DIFFRACTION7chain 'P' and (resid 13 through 18 )P13 - 18

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