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- PDB-6nyc: Munc13-1 C2B-domain, calcium free -

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Basic information

Entry
Database: PDB / ID: 6nyc
TitleMunc13-1 C2B-domain, calcium free
ComponentsMunc13-1
KeywordsMETAL 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: 1.893 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 / 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 11, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 20, 2019ID: 3KWT
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Munc13-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2904
Polymers16,9371
Non-polymers3533
Water36020
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)42.572, 101.141, 68.038
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 16937.131 Da / Num. of mol.: 1 / Fragment: C2B domain, residues 675-820 / 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.16 Å3/Da / Density % sol: 43.11 % / Mosaicity: 0.635 °
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, 0.5 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: 0.98066 Å
DetectorType: SBC-3 / Detector: CCD / Date: Nov 23, 2003 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98066 Å / Relative weight: 1
ReflectionResolution: 1.893→50 Å / Num. obs: 10420 / % possible obs: 86.5 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.05 / Χ2: 1.07 / Net I/σ(I): 17
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.9-1.933.30.3792790.993147.5
1.93-1.974.10.2943291.041155
1.97-2.014.40.2933461.001160.2
2.01-2.054.90.2284010.943166.4
2.05-2.095.50.2253861.086167.4
2.09-2.145.70.2034531.021174.8
2.14-2.196.10.1844661.068179.5
2.19-2.256.20.1735161.099187.3
2.25-2.326.60.1565491.059192.6
2.32-2.397.10.1425871.092197.7
2.39-2.487.80.1496011.1199.8
2.48-2.588.30.1355901.0921100
2.58-2.78.50.1075991.0891100
2.7-2.848.60.0856111.0991100
2.84-3.028.70.0635991.0761100
3.02-3.258.60.056121.0731100
3.25-3.588.50.046001.075199.8
3.58-4.098.50.0426111.0271100
4.09-5.1680.0376271.066199.8
5.16-26.437.90.0376581.072197.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RSY

1rsy


Resolution: 1.893→26.43 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 34.31
RfactorNum. reflection% reflection
Rfree0.2478 500 4.81 %
Rwork0.2091 --
obs0.211 10400 86.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.26 Å2 / Biso mean: 52.568 Å2 / Biso min: 20.37 Å2
Refinement stepCycle: final / Resolution: 1.893→26.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms942 0 47 20 1009
Biso mean--57.54 38.23 -
Num. residues----117
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8935-2.08390.2836810.22411649173059
2.0839-2.38530.26781260.21742434256086
2.3853-3.00460.28011320.25328662998100
3.0046-26.43230.23281610.192529513112100
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)
10.3239-0.3539-0.27230.78140.62920.69370.0841-0.37060.19730.22160.02070.4442-0.2007-0.2616-0.00080.2920.0462-0.01680.2630.00440.345914.308943.436432.7927
20.62670.3684-0.50091.48050.73491.1664-0.05030.0472-0.2591-0.0950.1118-0.3680.08990.04990.00170.2263-0.0219-0.01790.2498-0.05440.25520.257133.487330.8271
32.025-0.29470.19841.7791-0.60951.0010.04650.2189-0.6933-0.27330.0730.39340.3472-0.45160.06280.2529-0.0215-0.01410.3287-0.0960.240215.06431.17127.8389
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 780 through 819 )A780 - 819
2X-RAY DIFFRACTION2chain 'A' and (resid 687 through 737 )A687 - 737
3X-RAY DIFFRACTION3chain 'A' and (resid 738 through 779 )A738 - 779

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