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- PDB-4y21: Crystal Structure of Munc13-1 MUN domain -

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Basic information

Entry
Database: PDB / ID: 4y21
TitleCrystal Structure of Munc13-1 MUN domain
ComponentsProtein unc-13 homolog A
KeywordsEXOCYTOSIS / helical bundles / CATCHR
Function / homology
Function and homology information


dense core granule priming / neuronal dense core vesicle exocytosis / diacylglycerol binding / regulation of synaptic vesicle priming / presynaptic dense core vesicle exocytosis / synaptic vesicle docking / positive regulation of glutamate receptor signaling pathway / synaptic vesicle maturation / presynaptic active zone cytoplasmic component / positive regulation of synaptic plasticity ...dense core granule priming / neuronal dense core vesicle exocytosis / diacylglycerol binding / regulation of synaptic vesicle priming / presynaptic dense core vesicle exocytosis / synaptic vesicle docking / positive regulation of glutamate receptor signaling pathway / synaptic vesicle maturation / 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-1 binding / positive regulation of neurotransmitter secretion / syntaxin binding / synaptic vesicle priming / Golgi-associated vesicle / neuromuscular junction development / spectrin binding / presynaptic active zone / synaptic vesicle exocytosis / calyx of Held / excitatory synapse / 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 / protein domain specific binding / axon / glutamatergic synapse / synapse / calcium ion binding / protein-containing complex binding / protein-containing complex / identical protein binding / plasma membrane
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) / Phorbol esters/diacylglycerol binding domain (C1 domain) ...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) / 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
Protein unc-13 homolog A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsYang, X.Y. / Wang, S. / Sheng, Y. / Zhang, M. / Zou, W.J. / Wu, L.J. / Kang, L.J. / Rizo, J. / Zhang, R.G. / Xu, T. / Ma, C.
Funding support China, United States, 5items
OrganizationGrant numberCountry
National Science Foundation of China31370819 China
National Key Basic Research Program of China2014CB910203 China
National Science Foundation of China31130065 China
National Science Foundation of China91313301 China
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS37200 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Syntaxin opening by the MUN domain underlies the function of Munc13 in synaptic-vesicle priming.
Authors: Yang, X. / Wang, S. / Sheng, Y. / Zhang, M. / Zou, W. / Wu, L. / Kang, L. / Rizo, J. / Zhang, R. / Xu, T. / Ma, C.
History
DepositionFeb 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein unc-13 homolog A


Theoretical massNumber of molelcules
Total (without water)61,9871
Polymers61,9871
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area28390 Å2
Unit cell
Length a, b, c (Å)114.062, 270.921, 47.735
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: 61987.020 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 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q62768

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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: 5.9492 Å3/Da / Density % sol: 79.3248 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: PEG 3350, Mg(NO3)2, 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: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2011
RadiationMonochromator: SI(111) SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 34107 / % possible obs: 99.3 % / Redundancy: 5.4 % / Net I/σ(I): 27.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SWH

3swh


Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.934 / SU B: 30.556 / SU ML: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.348 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2519 1712 5.1 %RANDOM
Rwork0.2167 32104 --
obs0.2184 32104 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 247.41 Å2 / Biso mean: 88.522 Å2 / Biso min: 51.27 Å2
Baniso -1Baniso -2Baniso -3
1-3.75 Å2-0 Å20 Å2
2---0.44 Å20 Å2
3----3.32 Å2
Refinement stepCycle: final / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4347 0 0 0 4347
Num. residues----539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194436
X-RAY DIFFRACTIONr_bond_other_d0.0010.024277
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.975992
X-RAY DIFFRACTIONr_angle_other_deg0.7139892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0535537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.72725.24208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.41115833
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7021519
X-RAY DIFFRACTIONr_chiral_restr0.0690.2669
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214946
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02977
X-RAY DIFFRACTIONr_mcbond_it13.1367.9012154
X-RAY DIFFRACTIONr_mcbond_other13.1377.9012153
X-RAY DIFFRACTIONr_mcangle_it17.03611.9022689
LS refinement shellResolution: 2.896→2.971 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 123 -
Rwork0.341 2325 -
all-2448 -
obs--97.37 %
Refinement TLS params.Method: refined / Origin x: 90.3264 Å / Origin y: 57.0271 Å / Origin z: -9.8236 Å
111213212223313233
T0.4765 Å20.0524 Å2-0.0393 Å2-0.0275 Å20.0152 Å2--0.023 Å2
L0.5257 °2-0.6832 °20.4815 °2-0.8966 °2-0.6311 °2--0.4486 °2
S-0.0239 Å °-0.0086 Å °0.0293 Å °-0.006 Å °0.0082 Å °-0.0338 Å °-0.0124 Å °-0.0174 Å °0.0157 Å °

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