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- PDB-5uf7: CRYSTAL STRUCTURE OF MUNC13-1 MUN DOMAIN -

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Basic information

Entry
Database: PDB / ID: 5uf7
TitleCRYSTAL STRUCTURE OF MUNC13-1 MUN DOMAIN
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 / synaptic vesicle docking / regulation of synaptic vesicle priming / synaptic vesicle maturation / positive regulation of synaptic plasticity / positive regulation of glutamate receptor signaling pathway / positive regulation of dendrite extension / neurotransmitter secretion ...dense core granule priming / neuronal dense core vesicle exocytosis / diacylglycerol binding / synaptic vesicle docking / regulation of synaptic vesicle priming / synaptic vesicle maturation / positive regulation of synaptic plasticity / positive regulation of glutamate receptor signaling pathway / positive regulation of dendrite extension / neurotransmitter secretion / innervation / regulation of short-term neuronal synaptic plasticity / syntaxin binding / regulation of amyloid precursor protein catabolic process / syntaxin-1 binding / positive regulation of neurotransmitter secretion / Golgi-associated vesicle / synaptic vesicle priming / spectrin binding / neuromuscular junction development / synaptic vesicle exocytosis / presynaptic active zone / excitatory synapse / amyloid-beta metabolic process / calyx of Held / SNARE binding / synaptic transmission, glutamatergic / synaptic membrane / terminal bouton / neuromuscular junction / phospholipid binding / long-term synaptic potentiation / synaptic vesicle membrane / presynapse / presynaptic membrane / cell differentiation / calmodulin binding / protein domain specific binding / axon / synapse / calcium ion binding / protein-containing complex binding / glutamatergic synapse / protein-containing complex / zinc ion binding / 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) ...: / 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) / C2 domain / 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 / MOLECULAR REPLACEMENT / Resolution: 2.896 Å
Model detailsAlternatively spliced loop between residues 1407 and 1453 has been removed, addition of two ...Alternatively spliced loop between residues 1407 and 1453 has been removed, addition of two residues (EF) as cloning artifact.
AuthorsTomchick, D.R. / Rizo, J. / Xu, J.
Citation
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.
#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: 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
DepositionJan 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Revision 1.2Feb 21, 2018Group: Advisory / Database references / Category: citation / pdbx_database_PDB_obs_spr / Item: _citation.title
Revision 1.3Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.4Apr 13, 2022Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 27, 2022Group: Advisory / Category: pdbx_database_PDB_obs_spr
Revision 1.6Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 0This entry reflects an alternative modeling of the original data in 4Y21, determined by: Yang, X.Y. ...This entry reflects an alternative modeling of the original data in 4Y21, determined by: Yang, X.Y., Wang, S., Sheng, Y., Zhang, M., Zou, W.J., Wu, L.J., Kang, L.J., Rizo, J., Zhang, R.G., Xu, T., Ma, C.

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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


Theoretical massNumber of molelcules
Total (without water)62,8501
Polymers62,8501
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.062, 270.921, 47.735
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 62849.934 Da / Num. of mol.: 1 / Fragment: MUN DOMAIN (UNP residues 942-1407 and 1453-1531)
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: pGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q62768

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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: 5.95 Å3/Da / Density % sol: 79.33 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 4Y21.
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Mg(NO3)2, 0.1 M MES pH 5.8 - 6.3, 0.15 M NaCl, 18-25% PEG 3350, 10% glycerol, 5 mM DTT, 30% ethylene glycol
PH range: 5.8-6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2011 / Details: MONOCHROMATOR
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.896→39.018 Å / Num. obs: 34107 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 85.4 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 27.3
Reflection shellResolution: 2.896→2.95 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 1.95 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SWH

3swh


Resolution: 2.896→39.018 Å / SU ML: 0.38 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.28
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 1712 5.06 %random
Rwork0.2283 ---
obs0.2296 33801 99.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 293.18 Å2 / Biso mean: 112.1631 Å2 / Biso min: 45.65 Å2
Refinement stepCycle: final / Resolution: 2.896→39.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4281 0 0 0 4281
Num. residues----530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024368
X-RAY DIFFRACTIONf_angle_d0.4995900
X-RAY DIFFRACTIONf_chiral_restr0.032660
X-RAY DIFFRACTIONf_plane_restr0.003756
X-RAY DIFFRACTIONf_dihedral_angle_d10.6672684
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8959-2.98110.35241360.34522634277098
2.9811-3.07720.36981540.325925832737100
3.0772-3.18720.31781380.311927102848100
3.1872-3.31470.36471380.291225972735100
3.3147-3.46550.29841470.262926702817100
3.4655-3.64810.29011380.260426702808100
3.6481-3.87640.26911510.238526332784100
3.8764-4.17540.21671360.200826842820100
4.1754-4.5950.21591320.183227132845100
4.595-5.25860.20461510.17332695284699
5.2586-6.620.2931430.241727572900100
6.62-39.02170.22221480.22322743289194
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)
10.8173-0.84711.04531.1094-0.56230.91880.0415-0.0659-0.19150.39190.1804-0.1155-0.299-0.084700.7399-0.01490.04380.66240.03270.7884111.74066.718514.1977
20.027-0.4532-0.41720.6196-0.2940.2457-0.11230.0028-0.210.63410.24950.20230.107-0.003-00.6224-0.07880.01920.62330.05330.6244111.223929.656413.5654
30.8805-1.29120.40441.8098-2.08032.1911-0.05450.00050.0273-0.12960.09340.099-0.0978-0.167300.5276-0.0374-0.07360.59240.02610.5912102.639736.6616.9439
4-0.26720.01730.26540.78570.14020.243-0.34210.06620.39350.00790.0635-0.72130.0672-0.5956-0.01310.8670.2198-0.12830.85550.19130.951896.600867.1824-9.9782
5-0.3728-0.67760.46630.4563-0.49081.31390.05130.0467-0.1411-0.4598-0.03670.5389-0.0516-0.316400.77170.1908-0.14910.84320.15560.865884.646468.301-13.5991
6-0.00610.2752-0.21080.0869-0.4920.3074-0.7556-0.24140.27530.2964-0.0182-0.5648-0.49350.1413-0.00010.76960.0958-0.12060.74830.08920.784471.618897.7184-44.0503
70.0958-0.43260.49180.008-0.12280.40560.384-0.15560.3071-0.1312-0.294-0.29770.55910.0946-01.01260.2629-0.07330.89980.09440.834975.814583.0166-30.3084
81.004-0.26120.93330.4323-0.49020.8390.4230.35130.0591-0.0871-0.43520.0566-0.3834-0.695700.67120.0144-0.01220.72760.08620.608157.637894.2432-35.7305
9-0.0141-0.17210.2219-0.04210.1180.80270.4422-0.6517-0.7214-0.35310.06480.21571.0412-0.42830.00051.05380.13930.066210.20590.964262.068281.6827-38.2366
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 942:1000)A942 - 1000
2X-RAY DIFFRACTION2(chain A and resid 1001:1051)A1001 - 1051
3X-RAY DIFFRACTION3(chain A and resid 1052:1162)A1052 - 1162
4X-RAY DIFFRACTION4(chain A and resid 1163:1219)A1163 - 1219
5X-RAY DIFFRACTION5(chain A and resid 1220:1325)A1220 - 1325
6X-RAY DIFFRACTION6(chain A and resid 1326:1369)A1326 - 1369
7X-RAY DIFFRACTION7(chain A and resid 1370:1406)A1370 - 1406
8X-RAY DIFFRACTION8(chain A and resid 1407:1443)A1407 - 1443
9X-RAY DIFFRACTION9(chain A and resid 1444:1480)A1444 - 1480

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