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- PDB-8ban: Secretagogin (mouse) in complex with its target peptide from SNAP-25 -

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Basic information

Entry
Database: PDB / ID: 8ban
TitleSecretagogin (mouse) in complex with its target peptide from SNAP-25
Components
  • Green fluorescent protein,Synaptosomal-associated protein 25
  • Secretagogin
KeywordsPEPTIDE BINDING PROTEIN / Calcium-dependent / protein complex
Function / homology
Function and homology information


Toxicity of botulinum toxin type C (botC) / neurotransmitter uptake / Toxicity of botulinum toxin type E (botE) / 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 / presynaptic dense core vesicle exocytosis / extrinsic component of presynaptic membrane / Toxicity of botulinum toxin type A (botA) ...Toxicity of botulinum toxin type C (botC) / neurotransmitter uptake / Toxicity of botulinum toxin type E (botE) / 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 / presynaptic dense core vesicle exocytosis / extrinsic component of presynaptic membrane / Toxicity of botulinum toxin type A (botA) / ribbon synapse / synaptic vesicle docking / GABA synthesis, release, reuptake and degradation / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / SNAP receptor activity / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / SNARE complex / Glutamate Neurotransmitter Release Cycle / syntaxin-1 binding / Sensory processing of sound by inner hair cells of the cochlea / SNARE complex assembly / endosomal transport / Other interleukin signaling / synaptic vesicle priming / myosin binding / regulation of synapse assembly / transport vesicle membrane / regulation of neuron projection development / exocytosis / associative learning / synaptic vesicle exocytosis / tertiary granule membrane / voltage-gated potassium channel activity / long-term memory / specific granule membrane / axonal growth cone / voltage-gated potassium channel complex / photoreceptor inner segment / regulation of insulin secretion / axonogenesis / bioluminescence / filopodium / generation of precursor metabolites and energy / locomotory behavior / Regulation of insulin secretion / long-term synaptic potentiation / trans-Golgi network / positive regulation of insulin secretion / calcium-dependent protein binding / actin cytoskeleton / synaptic vesicle / lamellipodium / presynaptic membrane / growth cone / cell cortex / chemical synaptic transmission / transmembrane transporter binding / cytoskeleton / endosome / neuron projection / protein domain specific binding / neuronal cell body / lipid binding / calcium ion binding / Neutrophil degranulation / perinuclear region of cytoplasm / glutamatergic synapse / extracellular region / membrane / 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 / Green fluorescent protein, GFP ...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 / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / 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
Green fluorescent protein / Synaptosomal-associated protein 25 / Secretagogin
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Homo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSchnell, R. / Szodorai, E.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk Foundation Denmark
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: A hydrophobic groove in secretagogin allows for alternate interactions with SNAP-25 and syntaxin-4 in endocrine tissues.
Authors: Szodorai, E. / Hevesi, Z. / Wagner, L. / Hokfelt, T.G.M. / Harkany, T. / Schnell, R.
History
DepositionOct 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)122,66312
Polymers122,3434
Non-polymers3218
Water6,467359
1
A: Green fluorescent protein,Synaptosomal-associated protein 25
D: Secretagogin
hetero molecules


  • defined by author
  • Evidence: gel filtration, Confirming the sequence specific interaction observed in the crystal structure here between A-D chains and between B-C chains., isothermal titration calorimetry, Confirming ...Evidence: gel filtration, Confirming the sequence specific interaction observed in the crystal structure here between A-D chains and between B-C chains., isothermal titration calorimetry, Confirming the sequence specific interaction observed in the crystal structure here between A-D chains and between B-C chains.
  • 61.3 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)61,3326
Polymers61,1712
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green fluorescent protein,Synaptosomal-associated protein 25
C: Secretagogin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3326
Polymers61,1712
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.659, 121.068, 126.374
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Green fluorescent protein,Synaptosomal-associated protein 25 / SNAP-25 / Super protein / SUP / Synaptosomal-associated 25 kDa protein


Mass: 28980.629 Da / Num. of mol.: 2
Mutation: F64L,Q80R,I167T MUTATIONS IN ENHANCED GFP (HIGHER FLUORESCENCE INTENSITY)
Source method: isolated from a genetically manipulated source
Details: GFP-fusion protein carrying a short peptide from human SNAP25 (sequence: GIIGNLRHMALDMGNEIDTQNRQID) on its C-terminus. The Chromophore of GFP is formed from residues Ser65-Tyr66-Gly67, and ...Details: GFP-fusion protein carrying a short peptide from human SNAP25 (sequence: GIIGNLRHMALDMGNEIDTQNRQID) on its C-terminus. The Chromophore of GFP is formed from residues Ser65-Tyr66-Gly67, and represented as non-peptide residue CRO (Chromophore / Fluorophore). This alteration results in an apparent mismatch when comparing the encoded polypeptide sequence (present in databases) and the residues present in the PDB file.
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Homo sapiens (human)
Gene: GFP, SNAP25, SNAP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42212, UniProt: P60880
#2: Protein Secretagogin


Mass: 32190.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Scgn / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q91WD9
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.11 % / Description: rod
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: PEG 3350 (20%), 2 mM CaCl2, 0.1 M Bis-Tris-Propane pH 6.5, 25 mM Tris-HCl pH 8.0, 0.2 M NaI

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2020 / Details: Toroidal mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.35→87.42 Å / Num. obs: 46202 / % possible obs: 99.2 % / Observed criterion σ(I): 2.1 / Redundancy: 7.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Net I/σ(I): 11.9
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4186 / CC1/2: 0.72 / Rpim(I) all: 0.529 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EMA

1ema


Resolution: 2.35→87.42 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.787 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.422 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24816 2364 5.1 %RANDOM
Rwork0.19444 ---
obs0.19722 43747 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.655 Å2
Baniso -1Baniso -2Baniso -3
1--1.93 Å2-0 Å20 Å2
2--1.08 Å2-0 Å2
3---0.85 Å2
Refinement stepCycle: 1 / Resolution: 2.35→87.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8006 0 8 359 8373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0198170
X-RAY DIFFRACTIONr_bond_other_d0.0020.027772
X-RAY DIFFRACTIONr_angle_refined_deg1.731.96610981
X-RAY DIFFRACTIONr_angle_other_deg1.053317930
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4255980
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76924.952414
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.204151511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7131541
X-RAY DIFFRACTIONr_chiral_restr0.0950.21185
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029177
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021882
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6534.5513944
X-RAY DIFFRACTIONr_mcbond_other3.6534.5513943
X-RAY DIFFRACTIONr_mcangle_it5.46.8014913
X-RAY DIFFRACTIONr_mcangle_other5.46.8024914
X-RAY DIFFRACTIONr_scbond_it4.3115.0564226
X-RAY DIFFRACTIONr_scbond_other4.3075.0564226
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7137.3746067
X-RAY DIFFRACTIONr_long_range_B_refined9.92743.2434710
X-RAY DIFFRACTIONr_long_range_B_other9.93243.24634519
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 144 -
Rwork0.275 2957 -
obs--91.42 %

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