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- PDB-6ank: Synaptotagmin-7, C2A- and C2B-domains -

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Basic information

Entry
Database: PDB / ID: 6ank
TitleSynaptotagmin-7, C2A- and C2B-domains
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 / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.254 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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Synaptotagmin-7
B: Synaptotagmin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,57714
Polymers66,0082
Non-polymers56912
Water1,856103
1
A: Synaptotagmin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2897
Polymers33,0041
Non-polymers2846
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Synaptotagmin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2897
Polymers33,0041
Non-polymers2846
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.637, 75.059, 70.980
Angle α, β, γ (deg.)90.000, 114.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 33004.207 Da / Num. of mol.: 2 / Fragment: C2A-C2B domains (UNP residues 134-403)
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#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 / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 3350, 0.2 M lithium sulfate, 0.1 M Bis-Tris, 0.1 M calcium chloride, 0.125 M KCl, 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2015 / Details: monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.25→44.46 Å / Num. obs: 25080 / % possible obs: 91.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.046 / Net I/σ(I): 15.4
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 1.29 / % possible all: 56.3

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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: 3N5A, 6ANJ

3n5a

6anj


Resolution: 2.254→44.456 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.94
RfactorNum. reflection% reflectionSelection details
Rfree0.2568 2008 9.12 %random
Rwork0.2141 ---
obs0.218 22025 80.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.68 Å2 / Biso mean: 50.9553 Å2 / Biso min: 17.35 Å2
Refinement stepCycle: final / Resolution: 2.254→44.456 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4321 0 48 103 4472
Biso mean--79 39.62 -
Num. residues----525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144492
X-RAY DIFFRACTIONf_angle_d0.4895982
X-RAY DIFFRACTIONf_chiral_restr0.045657
X-RAY DIFFRACTIONf_plane_restr0.003748
X-RAY DIFFRACTIONf_dihedral_angle_d9.1122722
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2545-2.31080.3137450.302146851326
2.3108-2.37330.3286710.284469676740
2.3733-2.44310.3504890.28387396249
2.4431-2.5220.33161140.29691055116960
2.522-2.61210.30981210.29241223134470
2.6121-2.71670.31451460.28081474162082
2.7167-2.84030.34051760.27741726190297
2.8403-2.990.30221710.267717751946100
2.99-3.17730.32691800.253217771957100
3.1773-3.42260.26961800.225917741954100
3.4226-3.76680.25541840.1917881972100
3.7668-4.31150.20291830.177417791962100
4.3115-5.43050.17951780.14771791196999
5.4305-44.46460.23821700.19551818198898
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)
11.492-0.0423-0.59131.5550.35823.20320.492-0.3238-0.05470.451-0.4095-0.162-0.1750.0648-0.06380.4502-0.17050.01250.35620.07510.20768.796111.604756.4511
21.00310.1555-2.23281.01460.07116.25180.03610.0222-0.1970.3596-0.41640.2759-0.3929-0.76660.34010.3466-0.05680.03860.3452-0.00850.24722.92069.474851.6363
30.8422-0.436-0.21840.84890.50081.78690.25090.2276-0.06220.0331-0.31440.2354-0.86240.34040.0710.4963-0.03120.07610.32520.03250.29910.896317.840947.4415
41.18810.5520.35452.6538-0.05181.9111-0.0664-0.10470.0795-0.21220.0887-0.10610.03530.055-0.04510.2027-0.00220.04670.2297-0.06550.238-24.4918.942558.1309
51.1762-0.49580.11627.21615.35965.00560.31560.10780.2361-1.1960.01650.0236-0.3042-0.5026-0.23950.4064-0.07140.04640.2342-0.03710.2739-30.483216.35748.2004
61.99581.12580.0624.69432.5612.79770.14720.1355-0.3083-0.0896-0.0738-0.10190.0241-0.15850.18640.09520.0361-0.01080.2527-0.0710.2992-30.06616.21657.6708
72.03590.38080.37266.7397-0.1111.493-0.030.28470.0727-0.5621-0.02630.3160.0513-0.27010.12340.2870.01790.05420.2527-0.02630.2138-26.402218.469848.8439
81.93290.5940.22253.13820.72321.2780.11910.1216-0.2444-0.41270.0406-0.23440.45090.3207-0.08020.17270.04110.04050.2771-0.09850.2713-19.885710.892955.3502
91.7437-0.1727-0.65581.9792-0.32713.27520.259-0.15930.0770.6474-0.1678-0.02140.2176-0.23280.04310.3917-0.09110.01020.3154-0.0020.163253.689816.762324.0188
101.4375-0.0558-1.39011.2394-0.44364.17920.04860.0805-0.10850.1787-0.20020.44760.4162-0.51040.07230.3055-0.08390.07990.4069-0.0290.253147.847517.314619.1026
116.9853-4.4309-1.25934.7291-1.76544.0539-0.73950.01640.63210.0055-0.1581-0.1005-0.24680.34680.44010.27280.0737-0.01970.3553-0.01930.363262.874519.6667.5471
123.85280.6979-1.681.5204-0.22621.14480.72260.64240.4039-0.0376-0.1411-0.1669-0.3468-0.2081-0.31230.5458-0.0221-0.00120.3550.07930.397852.974924.81919.2393
132.26350.0272-0.44572.35460.57932.3897-0.35670.0235-0.2045-0.13280.04970.24930.20120.07210.31120.17650.0498-0.04170.18650.01360.268319.148411.70722.4113
140.84830.27940.42490.15860.32260.695-0.0623-0.14060.0937-0.0933-0.080.132-0.1418-0.1846-0.89230.06060.2423-0.30990.1541-0.1340.588712.478117.453120.3411
152.28820.1323-0.06122.55130.72322.8226-0.42820.2374-0.4782-0.1406-0.05290.23010.06330.25980.23790.190.06510.0260.2191-0.01490.386520.54248.76920.2659
163.83362.28270.89295.16510.32061.6906-0.25690.0242-0.9250.46510.2597-0.11210.22690.13720.19140.24920.28340.10380.24850.07310.359624.80446.547427.4922
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 135:206)A135 - 206
2X-RAY DIFFRACTION2(chain A and resid 207:233)A207 - 233
3X-RAY DIFFRACTION3(chain A and resid 234:259)A234 - 259
4X-RAY DIFFRACTION4(chain A and resid 266:306)A266 - 306
5X-RAY DIFFRACTION5(chain A and resid 307:326)A307 - 326
6X-RAY DIFFRACTION6(chain A and resid 327:344)A327 - 344
7X-RAY DIFFRACTION7(chain A and resid 345:362)A345 - 362
8X-RAY DIFFRACTION8(chain A and resid 363:402)A363 - 402
9X-RAY DIFFRACTION9(chain B and resid 135:208)B135 - 208
10X-RAY DIFFRACTION10(chain B and resid 209:243)B209 - 243
11X-RAY DIFFRACTION11(chain B and resid 244:249)B244 - 249
12X-RAY DIFFRACTION12(chain B and resid 250:267)B250 - 267
13X-RAY DIFFRACTION13(chain B and resid 268:315)B268 - 315
14X-RAY DIFFRACTION14(chain B and resid 316:327)B316 - 327
15X-RAY DIFFRACTION15(chain B and resid 328:391)B328 - 391
16X-RAY DIFFRACTION16(chain B and resid 392:403)B392 - 403

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