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

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Basic information

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


Toxicity of botulinum toxin type C (botC) / neurotransmitter uptake / Toxicity of botulinum toxin type E (botE) / GABA synthesis, release, reuptake and degradation / synaptic vesicle fusion to presynaptic active zone membrane / Toxicity of botulinum toxin type A (botA) / Acetylcholine Neurotransmitter Release Cycle / presynaptic dense core vesicle exocytosis / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / Serotonin Neurotransmitter Release Cycle ...Toxicity of botulinum toxin type C (botC) / neurotransmitter uptake / Toxicity of botulinum toxin type E (botE) / GABA synthesis, release, reuptake and degradation / synaptic vesicle fusion to presynaptic active zone membrane / Toxicity of botulinum toxin type A (botA) / Acetylcholine Neurotransmitter Release Cycle / presynaptic dense core vesicle exocytosis / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / Serotonin Neurotransmitter Release Cycle / synaptic vesicle docking / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / ribbon synapse / regulation of presynaptic cytosolic calcium ion concentration / Glutamate Neurotransmitter Release Cycle / SNARE complex / SNAP receptor activity / regulation of long-term synaptic potentiation / syntaxin-1 binding / Sensory processing of sound by inner hair cells of the cochlea / Other interleukin signaling / transport vesicle membrane / synaptic vesicle priming / regulation of neuron projection development / exocytosis / associative learning / tertiary granule membrane / synaptic vesicle exocytosis / voltage-gated potassium channel activity / specific granule membrane / somatodendritic compartment / photoreceptor inner segment / regulation of insulin secretion / bioluminescence / generation of precursor metabolites and energy / Regulation of insulin secretion / locomotory behavior / trans-Golgi network / long-term synaptic potentiation / terminal bouton / calcium-dependent protein binding / synaptic vesicle / presynaptic membrane / growth cone / cell cortex / chemical synaptic transmission / cytoskeleton / neuron projection / dendrite / calcium ion binding / synapse / lipid binding / Neutrophil degranulation / perinuclear region of cytoplasm / glutamatergic synapse / extracellular region / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Secretagogin, EF-hand domain / : / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / EF hand / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Green fluorescent protein, GFP ...Secretagogin, EF-hand domain / : / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / EF hand / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / 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
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / ACETATE ION / Secretagogin / Green fluorescent protein / Synaptosomal-associated protein 25
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 12, 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 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)122,69415
Polymers122,1334
Non-polymers56111
Water7,602422
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.
  • 61.4 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)61,4088
Polymers61,0662
Non-polymers3416
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)61,2867
Polymers61,0662
Non-polymers2195
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.544, 120.439, 124.066
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ABCD

#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
Source method: isolated from a genetically manipulated source
Details: GFP was engineered to carry the target peptide for the binding interaction. GFP-fusion protein carrying a short peptide from human SNAP25 (sequence: GIIGNLRHMALDMGNEIDTQNRQID) on its C- ...Details: GFP was engineered to carry the target peptide for the binding interaction. 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 datbases) 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: 32085.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCGN, SECRET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O76038

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Non-polymers , 4 types, 433 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.15 Å3/Da / Density % sol: 42.91 % / Description: rod
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M Na-acetate 20% PEG3350

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97996 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 28, 2020 / Details: Toroidal Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97996 Å / Relative weight: 1
ReflectionResolution: 2.3→41.36 Å / Num. obs: 47592 / % possible obs: 99.8 % / Observed criterion σ(I): 1.9 / Redundancy: 4.5 % / Biso Wilson estimate: 31.1 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.079 / Net I/σ(I): 9.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.702 / Num. unique obs: 4599 / CC1/2: 0.601 / Rpim(I) all: 0.545 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EMA, 8BAN

1ema

8ban


Resolution: 2.3→41.36 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.904 / SU B: 9 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.397 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26156 2449 5.2 %RANDOM
Rwork0.18772 ---
obs0.19149 45084 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.713 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å2-0 Å20 Å2
2--1.91 Å2-0 Å2
3----0.68 Å2
Refinement stepCycle: 1 / Resolution: 2.3→41.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8139 0 24 422 8585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198353
X-RAY DIFFRACTIONr_bond_other_d0.0020.027976
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.96711219
X-RAY DIFFRACTIONr_angle_other_deg0.964318386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33451007
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94924.654419
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.525151546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2151548
X-RAY DIFFRACTIONr_chiral_restr0.0820.21200
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029402
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021938
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_it2.5033.8284039
X-RAY DIFFRACTIONr_mcbond_other2.53.8274036
X-RAY DIFFRACTIONr_mcangle_it3.7445.7275038
X-RAY DIFFRACTIONr_mcangle_other3.7445.7275039
X-RAY DIFFRACTIONr_scbond_it3.2444.2144314
X-RAY DIFFRACTIONr_scbond_other3.2424.2144314
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1656.1516181
X-RAY DIFFRACTIONr_long_range_B_refined7.3636.39735694
X-RAY DIFFRACTIONr_long_range_B_other7.35536.40235464
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 175 -
Rwork0.263 3274 -
obs--99.42 %

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