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- PDB-5ue8: The crystal structure of Munc13-1 C1C2BMUN domain -

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Basic information

Entry
Database: PDB / ID: 5ue8
TitleThe crystal structure of Munc13-1 C1C2BMUN domain
ComponentsProtein unc-13 homolog A
KeywordsEXOCYTOSIS / ALPHA HELICAL / NEUROTRANSMITTER RELEASE / SNARE MOTIF / C1 DOMAIN / C2 DOMAIN
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 / SAD / MAD / molecular replacement / Resolution: 3.35 Å
Model detailsAlternatively spliced loop between residues 1407 and 1453 has been removed.
AuthorsTomchick, D.R. / Rizo, J. / Xu, J.
Citation
Journal: Elife / Year: 2017
Title: Mechanistic insights into neurotransmitter release and presynaptic plasticity from the crystal structure of Munc13-1 C1C2BMUN.
Authors: Xu, J. / Camacho, M. / Xu, Y. / Esser, V. / Liu, X. / Trimbuch, T. / Pan, Y.Z. / Ma, C. / Tomchick, D.R. / Rosenmund, C. / Rizo, J.
#1: Journal: Elife / Year: 2016
Title: Functional synergy between the Munc13 C-terminal C1 and C2 domains.
Authors: Liu, X. / Seven, A.B. / Camacho, M. / Esser, V. / Xu, J. / Trimbuch, T. / Quade, B. / Su, L. / Ma, C. / Rosenmund, C. / Rizo, J.
#2: Journal: 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.
#3: 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.
History
DepositionDec 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 2.0Feb 21, 2018Group: Database references / Polymer sequence / Category: citation / entity_poly / Item: _citation.title / _entity_poly.pdbx_target_identifier
Revision 2.1Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,7378
Polymers219,4042
Non-polymers3336
Water00
1
A: Protein unc-13 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,8684
Polymers109,7021
Non-polymers1663
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein unc-13 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,8684
Polymers109,7021
Non-polymers1663
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)176.145, 86.351, 202.142
Angle α, β, γ (deg.)90.000, 115.540, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 542 through 625 or resid 631...
21(chain B and (resid 542 through 800 or resid 808...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 542 through 625 or resid 631...A542 - 625
121(chain A and (resid 542 through 625 or resid 631...A631 - 702
131(chain A and (resid 542 through 625 or resid 631...A709 - 742
141(chain A and (resid 542 through 625 or resid 631...A746 - 758
151(chain A and (resid 542 through 625 or resid 631...A775 - 819
161(chain A and (resid 542 through 625 or resid 631...A825 - 922
171(chain A and (resid 542 through 625 or resid 631...A930 - 1337
181(chain A and (resid 542 through 625 or resid 631...A1353 - 1470
191(chain A and (resid 542 through 625 or resid 631...A1472 - 1515
211(chain B and (resid 542 through 800 or resid 808...B542 - 800
221(chain B and (resid 542 through 800 or resid 808...B808 - 922
231(chain B and (resid 542 through 800 or resid 808...B930 - 1037
241(chain B and (resid 542 through 800 or resid 808...B1053 - 1190
251(chain B and (resid 542 through 800 or resid 808...B1197 - 1403
261(chain B and (resid 542 through 800 or resid 808...B1470
271(chain B and (resid 542 through 800 or resid 808...B1472 - 1515

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Components

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


Mass: 109702.156 Da / Num. of mol.: 2
Fragment: C1C2BMUN domain (UNP residues 529-1407 and 1452-1531)
Mutation: L756W mutation. Removal of alternatively spliced loop between residues 1407 and 1453, addition of two residues (EF) as cloning artifact.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Unc13a, Unc13h1 / Plasmid: pFASTBac / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q62768
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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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: 3.14 Å3/Da / Density % sol: 60.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M LiCl, 0.1 M Tris-HCl pH 8.0, 0.15 M NaCl, 12% PEG 10,000, 10% glycerol, 5 mM TCEP, 25% ethylene glycol
PH range: 8.0 - 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 17, 2012 / Details: MONOCHROMATOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. obs: 37636 / % possible obs: 93.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 37.65 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.031 / Rrim(I) all: 0.064 / Χ2: 0.851 / Net I/σ(I): 9.9 / Num. measured all: 147746
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.35-3.413.30.69213630.8090.3880.7980.93868.9
3.41-3.473.40.62414600.850.3550.7220.96474
3.47-3.543.50.55116020.8660.3150.6380.92480.9
3.54-3.613.70.48116860.9010.2750.5560.92784.5
3.61-3.693.70.41617540.9230.2390.4810.96888.4
3.69-3.773.80.32818400.9590.1870.3790.93191.5
3.77-3.873.90.28318780.9640.1610.3270.93495.6
3.87-3.973.90.25519670.9710.1480.2960.96998.1
3.97-4.0940.19220040.9840.110.2220.90699.8
4.09-4.224.10.14219780.9930.080.1630.91899.9
4.22-4.374.10.10719840.9950.060.1230.90399.9
4.37-4.554.20.0820030.9970.0450.0920.875100
4.55-4.754.20.06619940.9970.0370.0760.805100
4.75-54.20.0520090.9980.0280.0580.761100
5-5.324.10.04919930.9980.0270.0560.797100
5.32-5.734.10.05420290.9950.030.0620.798100
5.73-6.34.10.0520290.9940.0280.0580.784100
6.3-7.2140.04120160.9950.0230.0470.847100
7.21-9.083.90.02320270.9980.0130.0270.727100
9.08-503.80.01620200.9980.0090.0190.51995.6

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Phasing

Phasing
Method
MAD
molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.35→45.598 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1490 4.98 %random
Rwork0.2524 28445 --
obs0.2542 29935 75.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 249.88 Å2 / Biso mean: 66.067 Å2 / Biso min: 8.21 Å2
Refinement stepCycle: final / Resolution: 3.35→45.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13597 0 6 0 13603
Biso mean--32.34 --
Num. residues----1685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313884
X-RAY DIFFRACTIONf_angle_d0.6118728
X-RAY DIFFRACTIONf_chiral_restr0.042088
X-RAY DIFFRACTIONf_plane_restr0.0042383
X-RAY DIFFRACTIONf_dihedral_angle_d11.4978409
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A9780X-RAY DIFFRACTION8.508TORSIONAL
12B9780X-RAY DIFFRACTION8.508TORSIONAL
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 (%)
3.35-3.45810.4435340.326575278622
3.4581-3.58170.3302610.30951017107830
3.5817-3.7250.2984820.30241520160245
3.725-3.89450.3079990.29152068216760
3.8945-4.09970.34561460.27362655280177
4.0997-4.35630.27851550.25313211336694
4.3563-4.69240.25231840.23534483632100
4.6924-5.1640.24211820.21734243606100
5.164-5.90990.27461800.256734193599100
5.9099-7.44060.34651820.290234823664100
7.4406-45.60240.28411850.21323449363497
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)
12.44110.28371.41230.17830.0530.898-0.02480.04430.1467-0.0738-0.1009-0.0732-0.09860.10860.08210.08040.0420.01390.4197-0.06310.26586.2233-28.8978164.3539
21.44160.59680.77780.53590.40010.91620.0052-0.36460.09830.14180.0143-0.0302-0.04940.02280.06660.27580.2351-0.08380.6602-0.04990.3009-11.7445-29.4582163.0982
31.1884-0.39310.38050.608-0.31780.65170.0321-0.0058-0.14640.0504-0.0225-0.24830.10930.15990.09250.18640.4083-0.19070.5047-0.01230.30845.1038-40.8834150.3957
40.64610.40220.93850.65550.18251.7802-0.10210.0960.0859-0.08710.2362-0.10390.19750.2509-0.0620.21750.10060.01750.74810.05570.2528-1.0295-40.3723120.4295
51.29240.40680.67541.36770.84012.5294-0.10020.0877-0.0535-0.2842-0.0161-0.0926-0.0513-0.01960.07690.5991-0.1736-0.00760.72770.19390.2894-8.0964-40.608288.5903
60.3786-0.03180.39360.0204-0.04380.8103-0.00230.09570.1022-0.2429-0.0309-0.0067-0.12070.01870.04641.35-0.32780.10780.96410.13860.4599-7.6746-37.936957.3435
70.94710.0843-0.47271.07490.31250.35420.04640.1589-0.012-0.1349-0.00980.0002-0.00870.0686-0.01061.7061-0.24040.22171.41070.23330.5624-0.8785-36.212441.2077
80.0273-0.0191-0.04630.02320.03740.08190.05570.21010.0647-0.09910.022-0.0421-0.05540.064-0.02992.0165-0.31080.43671.93980.13731.157210.3305-29.655217.025
90.06580.3453-0.12552.6262-0.2273.26340.03220.1003-0.0136-0.0108-0.04320.0867-0.0264-0.18870.01060.6924-0.1031-0.00970.3726-0.05430.2086-42.8293-36.5293-69.3063
100.67621.06570.22531.6870.36010.0788-0.0054-0.1603-0.21870.2642-0.0801-0.04230.18810.01380.05680.9643-0.21570.16030.91410.08170.7465-21.5776-21.96-84.5741
110.73010.0387-0.09080.7865-0.11790.79290.07780.3077-0.0253-0.17860.0798-0.0172-0.1144-0.1032-0.03611.0391-0.02220.16490.46290.09660.3527-40.092-24.6917-69.8101
120.34640.1706-0.19560.4195-0.25081.65520.00290.10910.0386-0.26250.1407-0.1223-0.11680.03140.00530.4255-0.02470.08890.1250.04470.2003-39.7933-26.2514-44.1622
130.73390.0198-0.51160.2755-0.02651.03190.0552-0.0447-0.0122-0.08630.0003-0.1038-0.09010.0724-0.00910.0286-0.25060.03120.16880.14140.1259-48.7522-28.5344-6.142
140.95750.16950.3990.76660.41731.12530.0549-0.187-0.11790.18380.0131-0.22860.05050.04610.00710.3212-0.242-0.08540.29610.01750.206-42.5081-28.218534.9698
150.15-0.1251-0.46830.12410.31941.76320.0519-0.1533-0.08870.19740.0441-0.1278-0.01260.21580.02760.94260.2626-0.39240.7168-0.01970.554-27.7398-22.58766.7737
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 541:611)A541 - 611
2X-RAY DIFFRACTION2(chain A and resid 612:687)A612 - 687
3X-RAY DIFFRACTION3(chain A and resid 688:892)A688 - 892
4X-RAY DIFFRACTION4(chain A and resid 893:1027)A893 - 1027
5X-RAY DIFFRACTION5(chain A and resid 1028:1160)A1028 - 1160
6X-RAY DIFFRACTION6(chain A and resid 1161:1244)A1161 - 1244
7X-RAY DIFFRACTION7(chain A and resid 1245:1324)A1245 - 1324
8X-RAY DIFFRACTION8(chain A and resid 1325:1517)A1325 - 1517
9X-RAY DIFFRACTION9(chain B and resid 542:566)B542 - 566
10X-RAY DIFFRACTION10(chain B and resid 567:624)B567 - 624
11X-RAY DIFFRACTION11(chain B and resid 625:856)B625 - 856
12X-RAY DIFFRACTION12(chain B and resid 857:1002)B857 - 1002
13X-RAY DIFFRACTION13(chain B and resid 1003:1161)B1003 - 1161
14X-RAY DIFFRACTION14(chain B and resid 1162:1322)B1162 - 1322
15X-RAY DIFFRACTION15(chain B and resid 1323:1515)B1323 - 1515

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