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- PDB-6nyt: Munc13-1 C2B-domain, calcium bound -

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Basic information

Entry
Database: PDB / ID: 6nyt
TitleMunc13-1 C2B-domain, calcium bound
ComponentsProtein unc-13 homolog A
KeywordsMETAL BINDING PROTEIN / CALCIUM BINDING PROTEIN / PHOSPHOLIPID BINDING PROTEIN
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) / C2 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) / C2 domain / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protein unc-13 homolog A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.369 Å
AuthorsTomchick, D.R. / Rizo, J. / Machius, M. / Lu, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS40944 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS051262 United States
Citation
Journal: Nat. Struct. Mol. Biol. / Year: 2010
Title: Munc13 C2B domain is an activity-dependent Ca2+ regulator of synaptic exocytosis.
Authors: Shin, O.H. / Lu, J. / Rhee, J.S. / Tomchick, D.R. / Pang, Z.P. / Wojcik, S.M. / Camacho-Perez, M. / Brose, N. / Machius, M. / Rizo, J. / Rosenmund, C. / Sudhof, T.C.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2004
Title: Calmodulin and Munc13 form a Ca2+ sensor/effector complex that controls short-term synaptic plasticity.
Authors: Junge, H.J. / Rhee, J.S. / Jahn, O. / Varoqueaux, F. / Speiss, J. / Waxham, M.N. / Rosenmund, C. / Brose, N.
#2: Journal: Nature / Year: 1999
Title: Munc-13 is essential for fusion competence of glutamatergic synaptic vesicles.
Authors: Augustin, I. / Rosenmund, C. / Sudhof, T.C. / Brose, N.
#3: Journal: J. Biol. Chem. / Year: 1995
Title: Mammalian homologues of C. elegans unc-13 gene define novel family of C2-domain proteins.
Authors: Brose, N. / Hofmann, K. / Hata, Y. / Sudhof, T.C.
History
DepositionFeb 12, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 20, 2019ID: 3KWU
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1806
Polymers16,9371
Non-polymers2435
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.943, 56.943, 89.983
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1146-

HOH

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Components

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


Mass: 16937.131 Da / Num. of mol.: 1 / Fragment: C2B / Mutation: L756W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Unc13a, Unc13h1 / Plasmid: pGEX-KT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q62768
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.14 Å3/Da / Density % sol: 42.44 % / Mosaicity: 0.484 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 30% PEG-MME 2000, 0.1 M bis-tris propane pH 6.8, 0.1 M NaCl, 0.1 MM CaCl2, 0.5 mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97895 Å
DetectorType: SBC-3 / Detector: AREA DETECTOR / Date: Jun 6, 2004 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 1.369→50 Å / Num. obs: 31875 / % possible obs: 99.8 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.055 / Χ2: 1.059 / Net I/σ(I): 15.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.37-1.395.90.46414830.973196.4
1.39-1.427.80.41515651.019199.7
1.42-1.459.20.39415451.0131100
1.45-1.4810.40.33515771.0641100
1.48-1.5111.50.28715621.0531100
1.51-1.5412.10.23915871.0421100
1.54-1.5812.40.20715811.0331100
1.58-1.6212.50.18115541.0611100
1.62-1.6712.60.15915851.0871100
1.67-1.7312.60.13215911.11100
1.73-1.7912.70.12615611.0861100
1.79-1.8612.60.10615861.0781100
1.86-1.9412.70.09215911.0721100
1.94-2.0512.60.07216031.0771100
2.05-2.1712.60.05915911.0711100
2.17-2.3412.60.05116011.0471100
2.34-2.5812.50.04916351.0581100
2.58-2.9512.20.04916271.051100
2.95-3.7211.80.03416661.0711100
3.72-30.00411.60.02817841.046199.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260: ???refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KWT

3kwt
PDB Unreleased entry


Resolution: 1.369→30.004 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 13.92
RfactorNum. reflection% reflection
Rfree0.169 1546 4.86 %
Rwork0.1478 --
obs0.1488 31808 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 67 Å2 / Biso mean: 20.8462 Å2 / Biso min: 6.6 Å2
Refinement stepCycle: final / Resolution: 1.369→30.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1097 0 18 146 1261
Biso mean--22.96 25.01 -
Num. residues----135
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.369-1.41320.19791340.17392612274698
1.4132-1.46370.22281400.142127152855100
1.4637-1.52230.1621340.122427052839100
1.5223-1.59160.15131280.123627412869100
1.5916-1.67550.16231320.11827312863100
1.6755-1.78040.15261480.124227092857100
1.7804-1.91790.15881310.123127492880100
1.9179-2.11090.1471500.128127472897100
2.1109-2.41620.13191730.137627412914100
2.4162-3.04370.17781390.174128232962100
3.0437-30.01110.19861370.166229893126100

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