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- PDB-8bbj: Secretagogin (mouse) in complex with its target peptide from Synt... -

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Basic information

Entry
Database: PDB / ID: 8bbj
TitleSecretagogin (mouse) in complex with its target peptide from Syntaxin-4
Components
  • Green fluorescent protein,Syntaxin-4
  • Secretagogin
KeywordsPEPTIDE BINDING PROTEIN / Calcium dependent / protein 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 / neuron projection membrane / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / vesicle-mediated transport in synapse / synaptic vesicle fusion to presynaptic active zone 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 / neuron projection membrane / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / vesicle-mediated transport in synapse / synaptic vesicle fusion to presynaptic active zone membrane / synaptic vesicle docking / storage vacuole / lateral loop / regulation of presynaptic cytosolic calcium ion concentration / vesicle fusion / myelin sheath adaxonal region / vesicle docking / SNARE complex / SNAP receptor activity / specific granule / positive regulation of chemotaxis / positive regulation of protein localization to cell surface / regulation of extrinsic apoptotic signaling pathway via death domain receptors / protein localization to cell surface / regulation of long-term synaptic potentiation / SNARE complex assembly / ER-Phagosome pathway / positive regulation of immunoglobulin production / transport vesicle membrane / exocytosis / 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 / phagocytic vesicle / bioluminescence / SNARE binding / generation of precursor metabolites and energy / 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 / cellular response to type II interferon / synaptic vesicle / 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 / synapse / calcium ion binding / dendrite / positive regulation of cell population proliferation / perinuclear region of cytoplasm / cell surface / extracellular space / extracellular region / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Secretagogin, EF-hand domain / 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 ...Secretagogin, EF-hand domain / 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 / 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
CACODYLATE ION / Green fluorescent protein / Syntaxin-4 / Secretagogin
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein,Syntaxin-4
B: Green fluorescent protein,Syntaxin-4
C: Secretagogin
D: Secretagogin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,32013
Polymers102,8634
Non-polymers4589
Water21612
1
A: Green fluorescent protein,Syntaxin-4
C: Secretagogin
hetero molecules


  • defined by author
  • Evidence: gel filtration, Confirming the sequence specific interaction observed in the crystal structure here between A-C chains and between B-D chains., isothermal titration calorimetry, Confirming ...Evidence: gel filtration, Confirming the sequence specific interaction observed in the crystal structure here between A-C chains and between B-D chains., isothermal titration calorimetry, Confirming the sequence specific interaction observed in the crystal structure here between A-C chains and between B-D chains.
  • 51.7 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)51,7297
Polymers51,4312
Non-polymers2975
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green fluorescent protein,Syntaxin-4
D: Secretagogin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5926
Polymers51,4312
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.409, 103.134, 121.656
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,Syntaxin-4


Mass: 29433.234 Da / Num. of mol.: 2 / Mutation: F64L,Q80R,I167T
Source method: isolated from a genetically manipulated source
Details: GFP-fusion protein carrying a short peptide from mouse Syntaxin-4 (sequence: GLQNLREEIKQLGREVRAQLKAIEPQKE) on its C-terminus. The Chromophore of GFP is formed from residues Ser65-Tyr66- ...Details: GFP-fusion protein carrying a short peptide from mouse Syntaxin-4 (sequence: GLQNLREEIKQLGREVRAQLKAIEPQKE) 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.) Mus musculus (house mouse)
Gene: GFP, Stx4, Stx4a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42212, UniProt: P70452
#2: Protein Secretagogin


Mass: 21998.104 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: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.55 Å3/Da / Density % sol: 72 % / Description: rod
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8
Details: 0.1 M Na cacodylate pH 5.5, 0.2 M NH4SO4, 25% v/v PEGSM (PEG-smear)

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 11, 2021 / Details: mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 2.65→78.68 Å / Num. obs: 28954 / % possible obs: 98.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 60.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.059 / Net I/σ(I): 8.2
Reflection shellResolution: 2.65→2.78 Å / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3847 / CC1/2: 0.598 / Rpim(I) all: 0.574

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EMA, 8BAN

1ema

8ban


Resolution: 2.65→48.289 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2685 1473 5.1 %
Rwork0.2132 --
obs0.216 28894 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→48.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6904 0 13 12 6929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047036
X-RAY DIFFRACTIONf_angle_d0.769465
X-RAY DIFFRACTIONf_dihedral_angle_d3.2334235
X-RAY DIFFRACTIONf_chiral_restr0.0461029
X-RAY DIFFRACTIONf_plane_restr0.0041231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6501-2.73560.35461440.32652479X-RAY DIFFRACTION99
2.7356-2.83340.3691470.30112474X-RAY DIFFRACTION99
2.8334-2.94680.35011190.28972488X-RAY DIFFRACTION98
2.9468-3.08090.35961240.27132484X-RAY DIFFRACTION98
3.0809-3.24330.29761600.24472466X-RAY DIFFRACTION98
3.2433-3.44640.32091250.22432504X-RAY DIFFRACTION98
3.4464-3.71240.26851050.22682523X-RAY DIFFRACTION98
3.7124-4.08590.27181390.19572466X-RAY DIFFRACTION97
4.0859-4.67670.2511390.17922511X-RAY DIFFRACTION97
4.6767-5.89050.20851270.18682488X-RAY DIFFRACTION96
5.8905-48.2890.24121440.1992538X-RAY DIFFRACTION93

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