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- PDB-6anj: Synaptotagmin-7, C2A domain -

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Basic information

Entry
Database: PDB / ID: 6anj
TitleSynaptotagmin-7, C2A domain
ComponentsSynaptotagmin-7
KeywordsPROTEIN BINDING / CALCIUM/PHOSPHOLIPID BINDING PROTEIN
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 / regulation of calcium ion-dependent exocytosis / exocytic vesicle / 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 / detection of calcium ion / GABA-ergic synapse / axon terminus / phagocytosis / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / hippocampal mossy fiber to CA3 synapse / cellular response to calcium ion / SNARE binding / terminal bouton / synaptic vesicle membrane / peroxisome / phagocytic vesicle membrane / synaptic vesicle / presynaptic membrane / lysosome / calmodulin binding / lysosomal membrane / dendrite / neuronal cell body / glutamatergic synapse / calcium ion binding / plasma membrane / cytosol
Similarity search - Function
Synaptotagmin 7, C2A domain / Synaptotagmin 7, C2B domain / Synaptotagmin / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulin-like ...Synaptotagmin 7, C2A domain / Synaptotagmin 7, C2B domain / Synaptotagmin / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / TERTIARY-BUTYL ALCOHOL / Synaptotagmin-7
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.698 Å
AuthorsTomchick, D.R. / Rizo, J. / Voleti, R.
Citation
Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Exceptionally tight membrane-binding may explain the key role of the synaptotagmin-7 C2A domain in asynchronous neurotransmitter release.
Authors: Voleti, R. / Tomchick, D.R. / Sudhof, T.C. / Rizo, J.
#1: Journal: PLoS ONE / Year: 2010
Title: Structural and mutational analysis of functional differentiation between synaptotagmins-1 and -7.
Authors: Xue, M. / Craig, T.K. / Shin, O.H. / Li, L. / Brautigam, C.A. / Tomchick, D.R. / Sudhof, T.C. / Rosenmund, C. / Rizo, J.
History
DepositionAug 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Synaptotagmin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2678
Polymers16,8651
Non-polymers4027
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.302, 55.302, 89.805
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Synaptotagmin-7 / / Protein Syt7 / Synaptotagmin VII / SytVII


Mass: 16865.297 Da / Num. of mol.: 1 / Fragment: C2A domain (UNP residues 134-262)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Syt7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q62747
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL / Tert-Butyl alcohol


Mass: 74.122 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.54 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 21% t-butanol, 0.1 M Tris, 0.1 M calcium chloride, 0.125 M KCl, 15% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2014 / Details: monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.698→27.651 Å / Num. obs: 17195 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 11.39 Å2 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.022 / Net I/σ(I): 34.6
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.985 / Mean I/σ(I) obs: 1.42 / CC1/2: 0.542 / Rpim(I) all: 0.528 / % possible all: 99.5

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D8K

2d8k


Resolution: 1.698→27.651 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.17
RfactorNum. reflection% reflectionSelection details
Rfree0.1811 1638 9.95 %random
Rwork0.1444 ---
obs0.148 16468 95.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.68 Å2 / Biso mean: 17.4537 Å2 / Biso min: 4.32 Å2
Refinement stepCycle: final / Resolution: 1.698→27.651 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1138 0 55 188 1381
Biso mean--28.21 30.03 -
Num. residues----138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171217
X-RAY DIFFRACTIONf_angle_d0.6751615
X-RAY DIFFRACTIONf_chiral_restr0.048172
X-RAY DIFFRACTIONf_plane_restr0.005206
X-RAY DIFFRACTIONf_dihedral_angle_d12.701722
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6977-1.74770.3432680.228765772551
1.7477-1.80410.28471360.19621263139998
1.8041-1.86850.19191400.164512901430100
1.8685-1.94330.19821410.157912681409100
1.9433-2.03180.18251410.133713171458100
2.0318-2.13880.17591430.12612841427100
2.1388-2.27280.15461450.126112771422100
2.2728-2.44820.16751440.123112941438100
2.4482-2.69430.20781470.138312881435100
2.6943-3.08380.20191420.14713041446100
3.0838-3.88350.16061470.130112771424100
3.8835-27.65470.15331440.15571311145599
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)
10.90120.08080.13191.2483-0.44920.39430.105-0.02520.20240.1962-0.1766-0.0168-0.04040.0002-0.09020.0841-0.0257-0.01940.1836-0.02580.127-1.952531.840420.4769
20.6643-0.2031-0.18310.5074-0.13811.55390.0055-0.0247-0.0312-0.03810.01820.04470.20910.0608-0.00380.07660.0195-0.03620.0437-0.01160.064718.723521.434125.9564
30.7083-0.0634-0.84360.4473-0.39962.53930.0471-0.08580.0950.06060.04890.0388-0.1959-0.0042-0.0470.05020.015-0.02020.0527-0.01120.084816.195428.434827.7679
40.6817-0.04010.15690.23320.38880.82620.0505-0.07880.0122-0.0387-0.00640.26150.0611-0.1622-0.03340.0898-0.0049-0.03220.11890.02260.13568.620422.133728.483
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -8 through 137 )A-8 - 137
2X-RAY DIFFRACTION2chain 'A' and (resid 138 through 210 )A138 - 210
3X-RAY DIFFRACTION3chain 'A' and (resid 211 through 244 )A211 - 244
4X-RAY DIFFRACTION4chain 'A' and (resid 245 through 262 )A245 - 262

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