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- PDB-1y8f: Solution structure of the munc13-1 C1-domain -

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Basic information

Entry
Database: PDB / ID: 1y8f
TitleSolution structure of the munc13-1 C1-domain
ComponentsUnc-13 homolog A
KeywordsENDOCYTOSIS/EXOCYTOSIS / SIGNALING PROTEIN / CYSTEINE-RICH DOMAIN / C1-DOMAIN / ZINC-BINDING DOMAIN / SIGNALING PROTEIN COMPLEX / ENDOCYTOSIS-EXOCYTOSIS
Function / homology
Function and homology information


dense core granule priming / neuronal dense core vesicle exocytosis / positive regulation of glutamate receptor signaling pathway / diacylglycerol binding / regulation of synaptic vesicle priming / presynaptic dense core vesicle exocytosis / synaptic vesicle docking / synaptic vesicle maturation / presynaptic active zone cytoplasmic component / positive regulation of synaptic plasticity ...dense core granule priming / neuronal dense core vesicle exocytosis / positive regulation of glutamate receptor signaling pathway / diacylglycerol binding / regulation of synaptic vesicle priming / presynaptic dense core vesicle exocytosis / synaptic vesicle docking / synaptic vesicle maturation / presynaptic active zone cytoplasmic component / positive regulation of synaptic plasticity / innervation / neurotransmitter secretion / positive regulation of dendrite extension / regulation of amyloid precursor protein catabolic process / regulation of short-term neuronal synaptic plasticity / syntaxin-1 binding / positive regulation of neurotransmitter secretion / synaptic vesicle priming / syntaxin binding / Golgi-associated vesicle / spectrin binding / neuromuscular junction development / 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 / phospholipid binding / neuromuscular junction / terminal bouton / synaptic vesicle membrane / presynapse / presynaptic membrane / cell differentiation / calmodulin binding / axon / protein domain specific binding / 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) / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 ...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) / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Phorbol esters/diacylglycerol binding domain (C1 domain) / C2 domain / Protein kinase C conserved region 2 (CalB) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain / C2 domain profile. / 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 / C1-like domain superfamily / C2 domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein unc-13 homolog A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsShen, N. / Guryev, O. / Rizo, J.
CitationJournal: Biochemistry / Year: 2005
Title: Intramolecular occlusion of the diacylglycerol-binding site in the C1 domain of munc13-1.
Authors: Shen, N. / Guryev, O. / Rizo, J.
History
DepositionDec 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Unc-13 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2473
Polymers7,1161
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 2000STRUCTURES WITH LOWEST NOE ENERGY
RepresentativeModel #1lowest noe energy

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Components

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


Mass: 7116.042 Da / Num. of mol.: 1 / Fragment: C1-domain (residues 567-616)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: MUNC13-1 / Plasmid: PGEX-KG / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q62768
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-separated NOESY
1313D 13C-separated NOESY
NMR detailsText: This structure was determined using standard triple resonance techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM munc13-1 C1-domain U-15N, 40mM HEPES (pH 7.0), 150mM NaCl, 50uM ZnCl240mM HEPES (pH 7.0), 150mM NaCl, 50uM ZnCl2
21.5mM munc13-1 C1-domain U-15N,13C, 40mM HEPES (pH 7.0), 150mM NaCl, 50uM ZnCl240 mM HEPES (pH 7.0), 150 mM NaCl, 50 uM ZnCl2
Sample conditionsIonic strength: 150mM NaCl / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe2.3Delaglioprocessing
NMRView4.1.2Johnsondata analysis
TALOS2003.027.13.05Delagliodata analysis
CNS0.9Brungerrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: A total of 861 restraints were used for the final calculations, including 781 NOEs (of which 384 were long-range NOEs), 30 hydrogen bond restraints, 50 torsion angle restraints and 18 ...Details: A total of 861 restraints were used for the final calculations, including 781 NOEs (of which 384 were long-range NOEs), 30 hydrogen bond restraints, 50 torsion angle restraints and 18 restraints for the two Zn2+ binding sites. The latter were derived from analysis of high resolution crystal structures containing bound Zn2+ ions that are coordinated by three cysteines and one histidine
NMR representativeSelection criteria: lowest noe energy
NMR ensembleConformer selection criteria: STRUCTURES WITH LOWEST NOE ENERGY
Conformers calculated total number: 2000 / Conformers submitted total number: 20

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