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- PDB-6lcy: Crystal structure of Synaptotagmin-7 C2B in complex with IP6 -

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Basic information

Entry
Database: PDB / ID: 6lcy
TitleCrystal structure of Synaptotagmin-7 C2B in complex with IP6
ComponentsSynaptotagmin-7
KeywordsEXOCYTOSIS / Synaptotagmin-7 / IP6 / Insulin secretion
Function / homology
Function and homology information


calcium ion regulated lysosome exocytosis / vesicle-mediated cholesterol transport / regulation of glucagon secretion / phagosome-lysosome fusion / short-term synaptic potentiation / synaptic vesicle recycling / calcium-dependent activation of synaptic vesicle fusion / regulation of bone remodeling / dense core granule / calcium ion-regulated exocytosis of neurotransmitter ...calcium ion regulated lysosome exocytosis / vesicle-mediated cholesterol transport / regulation of glucagon secretion / phagosome-lysosome fusion / short-term synaptic potentiation / synaptic vesicle recycling / calcium-dependent activation of synaptic vesicle fusion / regulation of bone remodeling / dense core granule / calcium ion-regulated exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis / vesicle fusion / regulation of calcium ion-dependent exocytosis / calcium-ion regulated exocytosis / plasma membrane repair / regulation of phagocytosis / calcium-dependent phospholipid binding / early phagosome / peroxisomal membrane / syntaxin binding / regulation of synaptic vesicle endocytosis / clathrin binding / phosphatidylserine binding / regulation of dopamine secretion / regulation of insulin secretion / GABA-ergic synapse / axon terminus / phagocytosis / phosphatidylinositol-4,5-bisphosphate binding / hippocampal mossy fiber to CA3 synapse / cellular response to calcium ion / SNARE binding / synaptic vesicle membrane / peroxisome / phagocytic vesicle membrane / synaptic vesicle / presynaptic membrane / lysosome / calmodulin binding / lysosomal membrane / axon / dendrite / neuronal cell body / glutamatergic synapse / synapse / calcium ion binding / plasma membrane / cytosol
Similarity search - Function
Synaptotagmin 7, C2A domain / Synaptotagmin 7, C2B domain / Synaptotagmin / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Synaptotagmin-7
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å
AuthorsZhang, Y. / Zhang, X. / Rao, F. / Wang, C.
CitationJournal: Nat Metab / Year: 2021
Title: 5-IP 7 is a GPCR messenger mediating neural control of synaptotagmin-dependent insulin exocytosis and glucose homeostasis.
Authors: Zhang, X. / Li, N. / Zhang, J. / Zhang, Y. / Yang, X. / Luo, Y. / Zhang, B. / Xu, Z. / Zhu, Z. / Yang, X. / Yan, Y. / Lin, B. / Wang, S. / Chen, D. / Ye, C. / Ding, Y. / Lou, M. / Wu, Q. / ...Authors: Zhang, X. / Li, N. / Zhang, J. / Zhang, Y. / Yang, X. / Luo, Y. / Zhang, B. / Xu, Z. / Zhu, Z. / Yang, X. / Yan, Y. / Lin, B. / Wang, S. / Chen, D. / Ye, C. / Ding, Y. / Lou, M. / Wu, Q. / Hou, Z. / Zhang, K. / Liang, Z. / Wei, A. / Wang, B. / Wang, C. / Jiang, N. / Zhang, W. / Xiao, G. / Ma, C. / Ren, Y. / Qi, X. / Han, W. / Wang, C. / Rao, F.
History
DepositionNov 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Synaptotagmin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7753
Polymers16,4551
Non-polymers1,3202
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-2 kcal/mol
Surface area7940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.406, 104.406, 53.404
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Synaptotagmin-7 / / Synaptotagmin VII / SytVII


Mass: 16455.207 Da / Num. of mol.: 1 / Fragment: C2B domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Syt7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9R0N7
#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 5.11 Å3/Da / Density % sol: 75.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100mM NaCl, 50mM Tris-Cl, 1mM EDTA, 1mM DDT, 5mM IP6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 14840 / % possible obs: 99.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 30.64 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.043 / Rrim(I) all: 0.09 / Χ2: 0.847 / Net I/σ(I): 10.3 / Num. measured all: 60777
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.343.90.5187240.8020.2980.61.002100
2.34-2.384.10.497290.8950.2680.560.94599.9
2.38-2.434.30.4197550.9060.2260.4770.922100
2.43-2.484.30.3777320.9110.2040.430.88100
2.48-2.534.20.3317380.9320.180.3780.89899.9
2.53-2.594.20.3197300.9370.1760.3650.941100
2.59-2.6640.2557550.9530.1430.2930.918100
2.66-2.733.90.2227350.9510.1250.2560.96599.6
2.73-2.814.20.27450.9620.1080.2280.85399.9
2.81-2.94.20.1737330.9680.0940.1980.83699.9
2.9-34.20.1227350.9820.0670.1390.85899.9
3-3.124.10.1017440.9830.0560.1160.87100
3.12-3.263.90.087500.9850.0450.0920.90899.7
3.26-3.444.20.0627260.990.0340.0720.88899.6
3.44-3.654.20.0517590.9920.0280.0590.82699.7
3.65-3.9340.0467360.9930.0260.0530.93599.7
3.93-4.3340.0367460.9940.020.0420.73798.9
4.33-4.954.20.0327520.9970.0170.0360.60799.5
4.95-6.2440.0327530.9960.0180.0370.58998.9
6.24-503.80.0357630.9940.0190.040.56496.7

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Processing

Software
NameVersionClassification
PHENIXv1.13refinement
PDB_EXTRACTdata extraction
MOLREP3.25phasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N5A

3n5a


Resolution: 2.301→45.209 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2387 740 5.03 %
Rwork0.2016 13973 -
obs0.2034 14713 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.88 Å2 / Biso mean: 33.0726 Å2 / Biso min: 13.93 Å2
Refinement stepCycle: final / Resolution: 2.301→45.209 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1120 0 84 34 1238
Biso mean--57.79 28.76 -
Num. residues----138
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.301-2.47840.31971560.2455266696
2.4784-2.72780.29931410.2482280699
2.7278-3.12240.23521350.23522829100
3.1224-3.93360.23081590.1952809100
3.9336-100.2041490.1666286399

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