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- PDB-3puj: Crystal structure of the MUNC18-1 and SYNTAXIN4 N-Peptide complex -

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Basic information

Entry
Database: PDB / ID: 3puj
TitleCrystal structure of the MUNC18-1 and SYNTAXIN4 N-Peptide complex
Components
  • Syntaxin-4 N-terminal peptide
  • Syntaxin-binding protein 1
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 / positive regulation of eosinophil degranulation / trans-Golgi Network Vesicle Budding / Other interleukin signaling / cornified envelope assembly / positive regulation of vesicle docking / regulation of acrosomal vesicle exocytosis / positive regulation of glutamate secretion, neurotransmission / neuron projection membrane ...sphingomyelin phosphodiesterase activator activity / Disinhibition of SNARE formation / positive regulation of eosinophil degranulation / trans-Golgi Network Vesicle Budding / Other interleukin signaling / cornified envelope assembly / positive regulation of vesicle docking / regulation of acrosomal vesicle exocytosis / positive regulation of glutamate secretion, neurotransmission / neuron projection membrane / negative regulation of SNARE complex assembly / regulation of vesicle fusion / developmental process involved in reproduction / axon target recognition / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / vesicle-mediated transport in synapse / extrinsic component of presynaptic membrane / synaptic vesicle fusion to presynaptic active zone membrane / regulation of synaptic vesicle priming / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / presynaptic dense core vesicle exocytosis / negative regulation of synaptic transmission, GABAergic / synaptic vesicle docking / storage vacuole / platelet degranulation / neuromuscular synaptic transmission / lateral loop / synaptic vesicle maturation / vesicle fusion / myelin sheath adaxonal region / vesicle docking / positive regulation of calcium ion-dependent exocytosis / SNARE complex / SNAP receptor activity / presynaptic active zone cytoplasmic component / specific granule / positive regulation of mast cell degranulation / positive regulation of chemotaxis / platelet alpha granule / neurotransmitter secretion / positive regulation of protein localization to cell surface / presynaptic cytosol / regulation of extrinsic apoptotic signaling pathway via death domain receptors / vesicle docking involved in exocytosis / protein localization to cell surface / parallel fiber to Purkinje cell synapse / long-term synaptic depression / syntaxin-1 binding / SNARE complex assembly / ER-Phagosome pathway / syntaxin binding / positive regulation of immunoglobulin production / synaptic vesicle priming / exocytosis / synaptic vesicle exocytosis / positive regulation of exocytosis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / phospholipase binding / positive regulation of cell adhesion / endomembrane system / negative regulation of protein-containing complex assembly / presynaptic active zone membrane / vesicle-mediated transport / phagocytic vesicle / SNARE binding / secretory granule / establishment of localization in cell / protein localization to plasma membrane / long-term synaptic potentiation / positive regulation of protein localization to plasma membrane / intracellular protein transport / Schaffer collateral - CA1 synapse / trans-Golgi network / terminal bouton / sarcolemma / small GTPase binding / platelet aggregation / cellular response to type II interferon / synaptic vesicle / presynapse / lamellipodium / response to estradiol / cellular response to oxidative stress / postsynapse / protein-containing complex assembly / basolateral plasma membrane / postsynaptic membrane / neuron apoptotic process / negative regulation of neuron apoptotic process / dendritic spine / molecular adaptor activity / membrane fusion / protein stabilization / endosome / positive regulation of cell migration
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-binding protein 1 / Syntaxin-4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.313 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.
CitationJournal: 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.
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
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 1
C: Syntaxin-4 N-terminal peptide
B: Syntaxin-binding protein 1
D: Syntaxin-4 N-terminal peptide


Theoretical massNumber of molelcules
Total (without water)138,0224
Polymers138,0224
Non-polymers00
Water00
1
A: Syntaxin-binding protein 1
C: Syntaxin-4 N-terminal peptide


Theoretical massNumber of molelcules
Total (without water)69,0112
Polymers69,0112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-28 kcal/mol
Surface area50480 Å2
2
B: Syntaxin-binding protein 1
D: Syntaxin-4 N-terminal peptide


Theoretical massNumber of molelcules
Total (without water)69,0112
Polymers69,0112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.505, 124.505, 232.976
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Syntaxin-binding protein 1 / N-Sec1 / Protein unc-18 homolog 1 / Unc18-1 / Protein unc-18 homolog A / Unc-18A / p67 / rbSec1


Mass: 67665.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stxbp1, Unc18a / Production host: Escherichia coli (E. coli) / References: UniProt: P61765
#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: 3.27 Å3/Da / Density % sol: 62.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 60% Tascimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2009
RadiationMonochromator: Saggittally focused Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 28009 / Num. obs: 26564 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 106.5 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 10.3
Reflection shellResolution: 3.3→3.43 Å / Redundancy: 6 % / Rmerge(I) obs: 0.796 / Mean I/σ(I) obs: 1.8 / Num. unique all: 2654 / % possible all: 96.8

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Processing

Software
NameVersionClassification
Blu-IceGuidata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DN1, Chain A

1dn1
PDB Unreleased entry


Resolution: 3.313→43.254 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8097 / SU ML: 0.39 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2576 1343 5.06 %RANDOM
Rwork0.2106 ---
obs0.2129 26560 94.8 %-
all-28009 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 109.111 Å2 / ksol: 0.315 e/Å3
Displacement parametersBiso max: 484.32 Å2 / Biso mean: 123.7 Å2 / Biso min: 56.85 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.78 Å / Luzzati d res low obs: 43.3 Å
Refinement stepCycle: LAST / Resolution: 3.313→43.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8638 0 0 0 8638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028789
X-RAY DIFFRACTIONf_angle_d0.55911870
X-RAY DIFFRACTIONf_dihedral_angle_d9.8413364
X-RAY DIFFRACTIONf_chiral_restr0.0381372
X-RAY DIFFRACTIONf_plane_restr0.0021501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
3.3133-3.43170.33181150.29472325244089
3.4317-3.5690.32441390.25012533267297
3.569-3.73140.31121270.22192497262496
3.7314-3.9280.23461380.21242500263896
3.928-4.17390.26531230.20852566268996
4.1739-4.49590.24071500.17582505265596
4.4959-4.94770.20921340.16992523265796
4.9477-5.66230.24161440.18952540268495
5.6623-7.12870.2381510.23112547269895
7.1287-43.25750.22771220.18512676266993
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)
13.32412.22230.57441.7452-0.54592.09710.0097-0.12250.39380.05980.0952-0.1533-0.45660.4243-0.08320.3443-0.1369-0.06740.60230.25841.1638.284244.0769-47.1714
22.7795-1.15530.40670.7414-1.14070.1142-0.22120.0706-0.1612-0.0051-0.1043-0.05590.02270.26530.35640.6411-0.03370.04570.72690.21511.08510.096818.4872-42.3593
32.64310.7934-0.4181.5030.20581.68330.1091-0.126-0.101-0.0524-0.25850.04880.1613-0.93410.08580.4069-0.10510.24520.96190.04721.0676-24.923926.6245-30.2735
43.78081.3115-0.74410.44140.40160.6879-0.19180.51070.242-0.09110.12680.0231-0.2064-0.0390.07210.4232-0.1765-0.00640.54010.19571.1079-12.785932.2892-47.8559
52.2691-1.55230.1111.829-0.34781.27330.03940.08370.28530.48850.2545-0.76960.37660.1571-0.23280.61370.2889-0.25220.5905-0.05131.07855.3852-16.2971-1.053
60.697-0.17941.01080.0011-0.76591.5380.08990.31970.4995-0.02120.0183-0.34070.21810.7678-0.12160.63050.29580.10080.81010.12421.456522.7617-16.0814-25.0655
71.4049-0.5477-0.12542.7552-0.15543.98140.8082-0.3293-0.26430.5166-0.7358-1.41-0.48231.66270.141-0.46610.69490.10180.6107-0.0271.108436.7104-20.3998-24.4328
80.5074-0.4515-0.45050.64460.59992.31030.048-0.13010.0223-0.81260.28690.0471-0.4821-0.2106-0.33210.9354-0.542-0.13121.70270.99830.761216.871553.6756-59.1131
90.753-1.472-0.09373.04560.21590.0376-0.56950.0658-1.6420.87450.36190.68160.2974-0.0741-0.14570.85240.1168-0.43180.61930.17071.83346.9482-29.98986.7628
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 3:211)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 212:357)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 358:478)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 479:590)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 4:139)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 140:386)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 387:591)
8X-RAY DIFFRACTION8(CHAIN C)
9X-RAY DIFFRACTION9(CHAIN D)

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