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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 / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / trans-Golgi Network Vesicle Budding / regulation of delayed rectifier potassium channel activity / diacylglycerol binding / regulation of calcium-dependent activation of synaptic vesicle fusion / Lysosome Vesicle Biogenesis / storage vacuole / zymogen granule membrane ...dense core granule priming / neuronal dense core vesicle exocytosis / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / trans-Golgi Network Vesicle Budding / regulation of delayed rectifier potassium channel activity / diacylglycerol binding / regulation of calcium-dependent activation of synaptic vesicle fusion / Lysosome Vesicle Biogenesis / storage vacuole / zymogen granule membrane / Other interleukin signaling / 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 / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / synaptic vesicle maturation / GABA synthesis, release, reuptake and degradation / hormone secretion / Dopamine Neurotransmitter Release Cycle / eosinophil degranulation / regulation of synaptic vesicle priming / Golgi Associated Vesicle Biogenesis / : / regulated exocytosis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / calcium-ion regulated exocytosis / positive regulation of neurotransmitter secretion / positive regulation of intracellular protein transport / regulation of vesicle-mediated transport / positive regulation of vesicle fusion / positive regulation of dendrite extension / Cargo recognition for clathrin-mediated endocytosis / regulation of exocytosis / Clathrin-mediated endocytosis / SNARE complex / SNAP receptor activity / vesicle fusion / positive regulation of synaptic plasticity / regulation of short-term neuronal synaptic plasticity / Golgi to plasma membrane protein transport / response to cholesterol / neurotransmitter secretion / innervation / regulation of amyloid precursor protein catabolic process / clathrin-coated vesicle / syntaxin binding / syntaxin-1 binding / presynaptic active zone / regulation of synaptic vesicle recycling / Golgi-associated vesicle / spectrin binding / myosin binding / SNARE complex assembly / positive regulation of glutamate receptor signaling pathway / neuron projection terminus / synaptic vesicle priming / amyloid-beta metabolic process / synaptic vesicle exocytosis / neuromuscular junction development / response to glucose / postsynaptic cytosol / synaptic vesicle endocytosis / vesicle-mediated transport / secretory granule / cytoplasmic vesicle membrane / excitatory synapse / calyx of Held / synaptic membrane / SNARE binding / synaptic transmission, glutamatergic / neuromuscular junction / trans-Golgi network / long-term synaptic potentiation / phospholipid binding / calcium-dependent protein binding / terminal bouton / cellular response to insulin stimulus / synaptic vesicle membrane / synaptic vesicle / protein transport / presynapse / protein-containing complex assembly / cytoplasmic vesicle / presynaptic membrane / vesicle / molecular adaptor activity / membrane fusion / transmembrane transporter binding / cell differentiation / calmodulin binding / postsynaptic density / protein domain specific binding / axon / calcium ion binding / lipid binding / synapse / protein-containing complex binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1100 / Tetracycline Repressor; domain 2 - #50 / 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 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1100 / Tetracycline Repressor; domain 2 - #50 / 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. / 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) / Tetracycline Repressor; domain 2 / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
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


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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