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- PDB-3puk: Re-refinement of the crystal structure of Munc18-3 and Syntaxin4 ... -

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Basic information

Entry
Database: PDB / ID: 3puk
TitleRe-refinement of the crystal structure of Munc18-3 and Syntaxin4 N-peptide complex
Components
  • Syntaxin-4 N-terminal peptide
  • Syntaxin-binding protein 3
KeywordsENDOCYTOSIS/EXOCYTOSIS / MEMBRANE TRAFFICKING / SM PROTEIN / SYNTAXIN / SNARE PROTEINS / Syntaxin binding protein / ENDOCYTOSIS-EXOCYTOSIS complex
Function / homology
Function and homology information


sphingomyelin phosphodiesterase activator activity / Disinhibition of SNARE formation / tertiary granule / positive regulation of eosinophil degranulation / trans-Golgi Network Vesicle Budding / Other interleukin signaling / cornified envelope assembly / neuron projection membrane / protein to membrane docking / exocytic insertion of neurotransmitter receptor to postsynaptic membrane ...sphingomyelin phosphodiesterase activator activity / Disinhibition of SNARE formation / tertiary granule / positive regulation of eosinophil degranulation / trans-Golgi Network Vesicle Budding / Other interleukin signaling / cornified envelope assembly / neuron projection membrane / protein to membrane docking / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / vesicle-mediated transport in synapse / synaptic vesicle fusion to presynaptic active zone membrane / neutrophil degranulation / synaptic vesicle docking / storage vacuole / lateral loop / vesicle fusion / myelin sheath adaxonal region / vesicle docking / negative regulation of calcium ion-dependent exocytosis / SNARE complex / SNAP receptor activity / specific granule / positive regulation of chemotaxis / platelet alpha granule / neurotransmitter secretion / negative regulation of glucose import / positive regulation of protein localization to cell surface / regulation of extrinsic apoptotic signaling pathway via death domain receptors / vesicle docking involved in exocytosis / protein localization to cell surface / insulin secretion / syntaxin-1 binding / SNARE complex assembly / ER-Phagosome pathway / syntaxin binding / positive regulation of immunoglobulin production / exocytosis / intracellular glucose homeostasis / synaptic vesicle exocytosis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of cell adhesion / endomembrane system / presynaptic active zone membrane / vesicle-mediated transport / phagocytic vesicle / SNARE binding / secretory granule / long-term synaptic potentiation / positive regulation of protein localization to plasma membrane / intracellular protein transport / Schaffer collateral - CA1 synapse / response to insulin / trans-Golgi network / brain development / sarcolemma / small GTPase binding / platelet aggregation / cellular response to type II interferon / synaptic vesicle / presynapse / lamellipodium / cellular response to oxidative stress / postsynapse / protein-containing complex assembly / basolateral plasma membrane / postsynaptic membrane / dendritic spine / membrane fusion / endosome / positive regulation of cell migration / apical plasma membrane / glutamatergic synapse / positive regulation of cell population proliferation / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / extracellular space / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #60 / Sec1/Munc18 (SM) protein, domain 2 / Syntaxin Binding Protein 1; Chain A, domain 2 / Sec1/Munc18 (SM) protein, domain 3a / Sec1/Munc18 (SM) protein, domain 1 / Sec1-like, domain 1 / Sec1-like, domain 2 / Sec1-like, domain 3a / Sec1-like protein / Sec1-like superfamily ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #60 / Sec1/Munc18 (SM) protein, domain 2 / Syntaxin Binding Protein 1; Chain A, domain 2 / Sec1/Munc18 (SM) protein, domain 3a / Sec1/Munc18 (SM) protein, domain 1 / Sec1-like, domain 1 / Sec1-like, domain 2 / Sec1-like, domain 3a / Sec1-like protein / Sec1-like superfamily / Sec1 family / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin / SNARE domain / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Syntaxin-4 / Syntaxin-binding protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.054 Å
AuthorsHu, S.-H. / Christie, M.P. / Saez, N.J. / Latham, C.F. / Jarrott, R. / Lua, L.H.L. / Collins, B.M. / Martin, J.L.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Possible roles for Munc18-1 domain 3a and Syntaxin1 N-peptide and C-terminal anchor in SNARE complex formation
Authors: Hu, S.-H. / Christie, M.P. / Saez, N.J. / Latham, C.F. / Jarrott, R. / Lua, L.H.L. / Collins, B.M. / Martin, J.L.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Structure of the Munc18c/Syntaxin4 N-peptide complex defines universal features of the N-peptide binding mode of Sec1/Munc18 proteins
Authors: Hu, S.H. / Latham, C.F. / Gee, C.L. / James, D.E. / Martin, J.L.
History
DepositionDec 5, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
SupersessionFeb 12, 2014ID: 2PJX
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Nov 1, 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: Syntaxin-binding protein 3
B: Syntaxin-binding protein 3
C: Syntaxin-4 N-terminal peptide
D: Syntaxin-4 N-terminal peptide


Theoretical massNumber of molelcules
Total (without water)138,7804
Polymers138,7804
Non-polymers00
Water00
1
A: Syntaxin-binding protein 3
C: Syntaxin-4 N-terminal peptide


Theoretical massNumber of molelcules
Total (without water)69,3902
Polymers69,3902
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Syntaxin-binding protein 3
D: Syntaxin-4 N-terminal peptide


Theoretical massNumber of molelcules
Total (without water)69,3902
Polymers69,3902
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.400, 170.400, 170.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Syntaxin-binding protein 3 / MUNC-18-3 / Mammalian homolog of Unc-18c / Munc-18c / Protein unc-18 homolog 3 / Unc18-3 / Protein ...MUNC-18-3 / Mammalian homolog of Unc-18c / Munc-18c / Protein unc-18 homolog 3 / Unc18-3 / Protein unc-18 homolog C / Unc-18C


Mass: 68044.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/c / Gene: Stxbp3, Stxbp3a, Unc18c / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q60770
#2: Protein/peptide Syntaxin-4 N-terminal peptide


Mass: 1345.531 Da / Num. of mol.: 2 / Fragment: UNP residues 1-10 / Source method: obtained synthetically / Details: Chemically synthesized peptide / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P70452

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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: 2.97 Å3/Da / Density % sol: 58.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10-13% PEG 3350, 0.2M MGACETATE, 0.1M MES, PH6.5, 50MM MGCL2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115872 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 6, 2006
RadiationMonochromator: SI (111) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115872 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. all: 31537 / Num. obs: 31147 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 99.7 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 15
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 1.7 / Num. unique all: 3132 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine)refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SQUID SEC1, PDB ENTRY 1EPU

1epu


Resolution: 3.054→45.541 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7256 / SU ML: 0.28 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 33.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1444 4.64 %RANDOM
Rwork0.2387 ---
obs0.2407 31147 98.68 %-
all-31537 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 143.481 Å2 / ksol: 0.305 e/Å3
Displacement parametersBiso max: 568.55 Å2 / Biso mean: 149.5 Å2 / Biso min: 58.59 Å2
Baniso -1Baniso -2Baniso -3
1--3.4499 Å2-0 Å2-0 Å2
2---3.4499 Å20 Å2
3----3.4499 Å2
Refinement stepCycle: LAST / Resolution: 3.054→45.541 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8521 0 0 0 8521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028674
X-RAY DIFFRACTIONf_angle_d0.60211749
X-RAY DIFFRACTIONf_dihedral_angle_d11.5073128
X-RAY DIFFRACTIONf_chiral_restr0.0421360
X-RAY DIFFRACTIONf_plane_restr0.0021510
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
3.0536-3.16270.3766200.31013064308498
3.1627-3.28930.32251580.28842937309599
3.2893-3.43890.3191570.27462937309499
3.4389-3.62020.35511520.27162945309799
3.6202-3.84690.29961660.2562937310399
3.8469-4.14370.28021630.24552882304597
4.1437-4.56040.30661540.20752940309498
4.5604-5.21950.24561800.19752945312598
5.2195-6.57280.28941540.2363011316599
6.5728-45.54640.21031400.20313105324599
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)
11.1654-0.0563-0.58370.9397-0.38721.1238-0.035-0.1254-0.26480.21710.27730.39590.7971-0.36780.01380.84240.21750.3470.83820.18260.7222-37.4175-65.1214115.6058
22.2859-0.1431-0.58241.33290.14832.10150.24460.29151.6214-0.46920.1809-0.81620.38740.3985-0.38740.24760.36770.39321.04070.0961.0024-17.1439-55.536102.6339
3-0.3467-0.2545-1.9412.2002-0.62262.08750.85660.1421.8415-0.2581-0.6403-0.8325-0.02921.2154-0.27780.54150.1652-0.24881.7319-0.45862.0868-6.6549-53.4167131.1952
4-1.15711.0018-0.1291.12340.5341-0.4220.20230.5091-0.6116-0.58510.4171-2.10550.00490.7159-0.3545-0.68260.94070.46721.5241-0.24811.25447.0083-58.2254111.6572
5-2.95950.32691.6179-0.3037-0.1754-0.18940.13260.41620.00650.1190.2083-0.1375-0.08140.552-0.18031.44030.12210.62752.2116-0.09562.00454.8531-43.9858103.0736
6-1.9433-1.52090.88011.59440.06741.644-0.02170.56281.16550.1640.1204-1.0797-0.49290.9991-0.31460.33940.09750.51811.12770.13751.944-11.6-48.5012105.4269
71.6176-0.28-0.16952.0538-0.45771.21620.21120.0180.13740.14140.1039-0.2423-0.0173-0.5855-0.07760.8430.3354-0.10490.5978-0.30990.5962-19.2809-73.5939189.0244
80.37580.17750.497-0.068-0.0084-0.4820.2144-0.05560.92750.39820.3248-0.8721-0.1616-0.16-0.00331.37850.38630.17910.25-0.0121.4586-10.5544-52.9983177.2404
90.6380.2105-0.17140.6465-1.19240.11910.7934-0.37531.30850.3328-0.4768-0.6309-0.49930.30470.16891.35540.48870.1951-0.2598-0.66581.6115-9.4913-39.9016194.1741
100.4688-0.9835-0.07660.2627-0.0718-0.46570.06050.09750.3828-0.46680.2252-1.2774-0.5226-0.0868-0.67930.99940.275-0.05240.3154-0.42021.5461-10.6676-54.1449190.758
11-0.9734-0.6740.75380.3794-2.2237.2712-0.1152-0.1068-0.0738-0.15260.48040.10830.3706-1.0249-0.33351.25950.38340.08221.28010.25521.0384-45.8882-60.496103.945
120.81940.7943-0.67061.5706-1.2423-0.45220.2267-0.1816-0.2354-0.5125-0.14290.03320.48570.1572-0.6591.60630.5256-0.52211.41010.02480.1888-18.1443-88.8825194.0969
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 7:140)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 141:270)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 271:314)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 315:450)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 451:470)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 471:585)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 7:221)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 222:351)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 352:524)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 525:585)
11X-RAY DIFFRACTION11(CHAIN C AND RESID 1:9)
12X-RAY DIFFRACTION12(CHAIN D AND RESID 1:10)

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