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- PDB-6jlh: Structure of SCGN in complex with a Snap25 peptide -

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Basic information

Entry
Database: PDB / ID: 6jlh
TitleStructure of SCGN in complex with a Snap25 peptide
Components
  • Secretagogin
  • Synaptosomal-associated protein 25SNAP25
KeywordsPROTEIN TRANSPORT / vesicle transport / endosomal sorting / membrane fusion
Function / homology
Function and homology information


Toxicity of botulinum toxin type C (botC) / neurotransmitter uptake / Toxicity of botulinum toxin type E (botE) / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Toxicity of botulinum toxin type A (botA) / Acetylcholine Neurotransmitter Release Cycle / extrinsic component of presynaptic membrane / synaptic vesicle fusion to presynaptic active zone membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex ...Toxicity of botulinum toxin type C (botC) / neurotransmitter uptake / Toxicity of botulinum toxin type E (botE) / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Toxicity of botulinum toxin type A (botA) / Acetylcholine Neurotransmitter Release Cycle / extrinsic component of presynaptic membrane / synaptic vesicle fusion to presynaptic active zone membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / presynaptic dense core vesicle exocytosis / ribbon synapse / spinal cord motor neuron differentiation / synaptic vesicle docking / Dopamine Neurotransmitter Release Cycle / regulation of presynaptic cytosolic calcium ion concentration / Norepinephrine Neurotransmitter Release Cycle / SNARE complex / SNAP receptor activity / Glutamate Neurotransmitter Release Cycle / neurotransmitter receptor internalization / regulation of long-term synaptic potentiation / Sensory processing of sound by inner hair cells of the cochlea / syntaxin-1 binding / SNARE complex assembly / synaptic vesicle priming / regulation of synapse assembly / endosomal transport / Other interleukin signaling / myosin binding / regulation of neuron projection development / exocytosis / synaptic vesicle exocytosis / voltage-gated potassium channel activity / tertiary granule membrane / associative learning / regulation of insulin secretion / long-term memory / specific granule membrane / voltage-gated potassium channel complex / axonal growth cone / presynaptic active zone membrane / photoreceptor inner segment / axonogenesis / locomotory behavior / filopodium / long-term synaptic potentiation / Regulation of insulin secretion / brain development / trans-Golgi network / terminal bouton / positive regulation of insulin secretion / calcium-dependent protein binding / synaptic vesicle / actin cytoskeleton / presynaptic membrane / lamellipodium / cell cortex / growth cone / chemical synaptic transmission / postsynapse / transmembrane transporter binding / cytoskeleton / endosome / neuron projection / protein domain specific binding / neuronal cell body / dendrite / synapse / glutamatergic synapse / lipid binding / calcium ion binding / Neutrophil degranulation / perinuclear region of cytoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Secretagogin, EF-hand domain / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / EF hand / EF-hand domain pair / EF-hand, calcium binding motif ...Secretagogin, EF-hand domain / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / EF hand / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Synaptosomal-associated protein 25 / Secretagogin
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.37 Å
AuthorsQin, J. / Sun, Q. / Jia, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural and mechanistic insights into secretagogin-mediated exocytosis.
Authors: Qin, J. / Liu, Q. / Liu, Z. / Pan, Y.Z. / Sifuentes-Dominguez, L. / Stepien, K.P. / Wang, Y. / Tu, Y. / Tan, S. / Wang, Y. / Sun, Q. / Mo, X. / Rizo, J. / Burstein, E. / Jia, D.
History
DepositionMar 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Secretagogin
B: Synaptosomal-associated protein 25
C: Secretagogin
D: Synaptosomal-associated protein 25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,90617
Polymers65,3904
Non-polymers51613
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-137 kcal/mol
Surface area27410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.524, 107.049, 54.770
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 Secretagogin / / SCGN


Mass: 30864.705 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: scgn, zgc:100843 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5XJX1
#2: Protein/peptide Synaptosomal-associated protein 25 / SNAP25 / SNAP-25


Mass: 1830.097 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAP25, SNAP / Production host: Escherichia coli (E. coli) / References: UniProt: P60880
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M glycocine, 0.1 M Tris Bicine pH 8.5, 12.5% MPD, 12.5% PEG 1000, 12.5% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97921 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. obs: 25808 / % possible obs: 99.6 % / Redundancy: 37.4 % / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.035 / Rrim(I) all: 0.197 / Χ2: 0.997 / Net I/σ(I): 4.6 / Num. measured all: 964927
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.37-2.4120.911670.6390.3420.93391.8
2.41-2.4533.412620.8140.2670.937100
2.45-2.536.712880.8720.2340.956100
2.5-2.5538.512450.8910.2110.952100
2.55-2.613912930.9230.1790.973100
2.61-2.6739.212430.9350.1610.982100
2.67-2.7438.712960.9420.1381.0091000.8480.859
2.74-2.8136.712710.9560.1171.0161000.70.709
2.81-2.8938.213050.9660.1031.0491000.6290.637
2.89-2.9940.612590.9760.0831.0711000.5190.525
2.99-3.0940.213070.9820.0671.0741000.420.426
3.09-3.2239.712610.9850.0571.0951000.3530.358
3.22-3.3638.312940.9850.051.1151000.3030.307
3.36-3.5436.512870.9920.0431.1081000.2540.257
3.54-3.7640.113010.9920.0351.0931000.2180.221
3.76-4.0539.713120.9910.0321.0161000.1940.197
4.05-4.4638.113090.9910.0290.9791000.1720.175
4.46-5.138.613230.9950.0240.8621000.150.152
5.1-6.4338.413410.9970.0230.7451000.1410.142
6.43-5034.914440.9910.0290.9421000.1670.17

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
AutoSolphasing
RefinementResolution: 2.37→46.96 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.903 / SU B: 16.856 / SU ML: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.552 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2372 1950 8 %RANDOM
Rwork0.2003 ---
obs0.2034 22304 94.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.96 Å2 / Biso mean: 38.087 Å2 / Biso min: 16.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0 Å2-0 Å2
2---0.06 Å20 Å2
3---0.16 Å2
Refinement stepCycle: final / Resolution: 2.37→46.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4482 0 13 142 4637
Biso mean--41.21 34.06 -
Num. residues----551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134562
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174283
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.6466107
X-RAY DIFFRACTIONr_angle_other_deg1.2481.5939973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4085547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.09123.433268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.07115834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2861528
X-RAY DIFFRACTIONr_chiral_restr0.0730.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025079
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02949
LS refinement shellResolution: 2.367→2.429 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 89 -
Rwork0.261 955 -
all-1044 -
obs--56.55 %
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)
10.9624-0.4389-0.03280.73290.23630.21730.07740.0945-0.14570.088-0.02680.099-0.0123-0.0296-0.05060.07710.03390.02830.0783-0.00030.060452.858625.19138.6264
21.77762.7516-2.46879.9459-5.73524.5638-0.0296-0.01120.03060.14110.0663-0.24440.01160.0128-0.03670.04410.0371-0.03710.0667-0.04670.054874.755414.853810.2054
31.15990.4937-0.23820.8443-0.64120.511-0.0291-0.10480.085-0.0298-0.0106-0.0140.02180.01150.03970.10730.00320.0370.05870.00990.032263.502531.914123.143
48.2331-5.7079-0.46799.61750.99060.1051-0.16120.17030.0401-0.40330.14860.0183-0.05070.02290.01270.089-0.027-0.00770.13250.07360.043567.797644.2993-0.2492
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 307
2X-RAY DIFFRACTION2B1 - 17
3X-RAY DIFFRACTION3C12 - 306
4X-RAY DIFFRACTION4D1 - 17

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