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- PDB-3swh: Munc13-1, MUN domain, C-terminal module -

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Basic information

Entry
Database: PDB / ID: 3swh
TitleMunc13-1, MUN domain, C-terminal module
ComponentsProtein unc-13 homolog A
KeywordsEXOCYTOSIS / alpha helical / neurotransmitter release / SNARE motif
Function / homology
Function and homology information


dense core granule priming / neuronal dense core vesicle exocytosis / diacylglycerol binding / presynaptic dense core vesicle exocytosis / synaptic vesicle docking / regulation of synaptic vesicle priming / synaptic vesicle maturation / positive regulation of glutamate receptor signaling pathway / presynaptic active zone cytoplasmic component / positive regulation of synaptic plasticity ...dense core granule priming / neuronal dense core vesicle exocytosis / diacylglycerol binding / presynaptic dense core vesicle exocytosis / synaptic vesicle docking / regulation of synaptic vesicle priming / synaptic vesicle maturation / positive regulation of glutamate receptor signaling pathway / 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 binding / syntaxin-1 binding / positive regulation of neurotransmitter secretion / synaptic vesicle priming / Golgi-associated vesicle / neuromuscular junction development / spectrin binding / presynaptic active zone / synaptic vesicle exocytosis / excitatory synapse / calyx of Held / 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 / calcium ion binding / synapse / protein-containing complex binding / protein-containing complex / identical protein binding / plasma membrane
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1100 / Tetracycline Repressor; domain 2 - #50 / : / 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 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1100 / Tetracycline Repressor; domain 2 - #50 / : / 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. / 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 / Tetracycline Repressor; domain 2 / 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
Protein unc-13 homolog A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.65 Å
AuthorsTomchick, D.R. / Rizo, J. / Li, W.
Citation
Journal: Structure / Year: 2011
Title: The Crystal Structure of a Munc13 C-terminal Module Exhibits a Remarkable Similarity to Vesicle Tethering Factors.
Authors: Li, W. / Ma, C. / Guan, R. / Xu, Y. / Tomchick, D.R. / Rizo, J.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Munc13 mediates the transition from the closed syntaxin-Munc18 complex to the SNARE complex.
Authors: Ma, C. / Li, W. / Xu, Y. / Rizo, J.
History
DepositionJul 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
B: Protein unc-13 homolog A


Theoretical massNumber of molelcules
Total (without water)77,4732
Polymers77,4732
Non-polymers00
Water1,78399
1
A: Protein unc-13 homolog A


Theoretical massNumber of molelcules
Total (without water)38,7371
Polymers38,7371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein unc-13 homolog A


Theoretical massNumber of molelcules
Total (without water)38,7371
Polymers38,7371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)160.791, 160.791, 42.239
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42

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Components

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


Mass: 38736.520 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Unc13a, Unc13h1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q62768
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN FRAGMENT COMPRISES UNP Q62768 RESIDUES 1148-1407 AND 1453-1531 CONNECTED BY AN ENGINEERED EF LINKER.

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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: 3.52 Å3/Da / Density % sol: 65.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 18-25% PEG400, 0.1 M MES, pH 6.0, 0.15 M sodium chloride, 10% glycerol, 5 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97178, 0.97945, 0.97959
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.971781
20.979451
30.979591
ReflectionResolution: 2.65→50 Å / Num. all: 28911 / Num. obs: 28911 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.075 / Χ2: 1.236 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.65-2.73.30.67413991.379190.7
2.7-2.743.70.72414730.874191.9
2.74-2.84.20.60814790.931192.6
2.8-2.854.40.53814610.95192.2
2.85-2.924.50.48514470.945191.8
2.92-2.984.60.42314770.96192.5
2.98-3.064.60.30614501.054192.1
3.06-3.144.60.2614571.091191.7
3.14-3.234.80.21414981.121192.5
3.23-3.344.60.16114321.24191.5
3.34-3.464.60.15114611.618191.3
3.46-3.64.70.11914581.336191.5
3.6-3.764.60.09814471.543190.4
3.76-3.964.60.08214511.564190.1
3.96-4.214.80.06314611.347190.1
4.21-4.534.70.0614261.444189.7
4.53-4.994.80.05914311.306188.2
4.99-5.714.70.0614411.391188.1
5.71-7.194.60.04614411.318186.8
7.19-5050.03413211.222176.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.65→29.119 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6931 / SU ML: 0.78 / Isotropic thermal model: ISOTROPIC OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 35.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3016 1446 5.02 %RANDOM
Rwork0.244 ---
all0.2469 28794 --
obs0.2469 28794 89.63 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.902 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso max: 211.19 Å2 / Biso mean: 80.1854 Å2 / Biso min: 24.43 Å2
Baniso -1Baniso -2Baniso -3
1--11.4827 Å2-0 Å20 Å2
2---11.4827 Å2-0 Å2
3---22.9654 Å2
Refine analyzeLuzzati sigma a obs: 0.78 Å
Refinement stepCycle: LAST / Resolution: 2.65→29.119 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4753 0 0 99 4852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094836
X-RAY DIFFRACTIONf_angle_d1.226516
X-RAY DIFFRACTIONf_chiral_restr0.075744
X-RAY DIFFRACTIONf_plane_restr0.005829
X-RAY DIFFRACTIONf_dihedral_angle_d15.6851829
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6498-2.74440.33891480.30522661280990
2.7444-2.85420.37981720.3052771294392
2.8542-2.9840.35141420.29792779292192
2.984-3.14110.33931180.25712773289192
3.1411-3.33770.34641520.26322801295392
3.3377-3.59490.3491320.26672782291491
3.5949-3.95590.3191390.26622728286789
3.9559-4.52650.28261570.22562736289390
4.5265-5.69590.26171680.22032707287588
5.6959-29.12070.25481180.20462610272881
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)
11.1426-0.13860.24830.5087-0.21771.1492-0.06650.10410.0892-0.01080.0862-0.0278-0.02830.27130.26770.4643-0.0009-0.35910.83350.26650.56178.908539.8619-2.4402
29.16371.33481.34715.78693.67882.5180.4317-1.1393-0.57540.2725-0.41410.6838-0.0045-0.28250.01830.55480.2273-0.13510.85630.09520.496658.182534.448710.3274
32.3153-0.18780.65370.7150.02771.67-0.14480.44360.16930.00760.1516-0.1437-0.01340.4435-0.02170.5429-0.0346-0.27530.81590.19740.394368.845537.6045-10.2787
45.44741.61150.32284.03850.87161.601-0.0256-0.47510.37950.7385-0.04851.15340.0306-0.0607-0.00450.60110.08750.07830.42530.23880.69940.613829.82367.9756
51.50221.2380.36912.7770.40751.8259-0.20460.02710.13760.02860.16140.75130.1641-0.1832-0.1090.39240.00050.0160.51320.40030.873538.000825.5175-2.1726
61.88790.2585-0.01761.59190.12170.9921-0.120.1772-0.2432-0.0532-0.01880.4277-0.0915-0.4515-0.21380.37960.1408-0.32080.8260.15230.73081.997140.93-23.574
78.228-0.2675-2.28468.1749-1.00340.77670.1163-0.2110.33940.5437-0.1031-0.5868-0.15650.09510.02860.29030.0705-0.08590.67240.18340.749920.425744.4457-15.5031
85.31112.87854.51873.2031.72175.2926-0.0661.1089-0.7273-0.31250.28090.2414-0.05550.1129-0.21190.34610.1349-0.13381.02860.06040.83079.911442.2317-34.0794
93.4263-0.10770.61111.8305-0.07761.282-0.01950.1091-0.07210.1999-0.145-0.2249-0.24050.17030.09820.42330.0716-0.22620.54790.30640.745539.830850.9345-13.3134
101.3137-0.0141-0.7021.6305-0.59311.54040.17290.06080.02490.0591-0.3235-0.5676-0.31550.46940.14280.36990.0072-0.00940.57090.42490.850342.965154.4523-23.4632
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1156:1256)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 1257:1270)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 1271:1315)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 1316:1384)A0
5X-RAY DIFFRACTION5chain 'A' and (resseq 1385:1514)A0
6X-RAY DIFFRACTION6chain 'B' and (resseq 1156:1256)B0
7X-RAY DIFFRACTION7chain 'B' and (resseq 1257:1277)B0
8X-RAY DIFFRACTION8chain 'B' and (resseq 1278:1311)B0
9X-RAY DIFFRACTION9chain 'B' and (resseq 1312:1381)B0
10X-RAY DIFFRACTION10chain 'B' and (resseq 1382:1516)B0

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