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- PDB-3n5a: Synaptotagmin-7, C2B-domain, calcium bound -

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Basic information

Entry
Database: PDB / ID: 3n5a
TitleSynaptotagmin-7, C2B-domain, calcium bound
ComponentsSynaptotagmin-7
KeywordsPROTEIN TRANSPORT / 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 / synaptic vesicle recycling / calcium-dependent activation of synaptic vesicle fusion / short-term synaptic potentiation / regulation of bone remodeling / dense core granule / regulation of calcium ion-dependent exocytosis ...calcium ion regulated lysosome exocytosis / vesicle-mediated cholesterol transport / regulation of glucagon secretion / phagosome-lysosome fusion / synaptic vesicle recycling / calcium-dependent activation of synaptic vesicle fusion / short-term synaptic potentiation / regulation of bone remodeling / dense core granule / regulation of calcium ion-dependent exocytosis / calcium ion-regulated exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis / vesicle fusion / calcium-ion regulated exocytosis / plasma membrane repair / regulation of phagocytosis / calcium-dependent phospholipid binding / early phagosome / syntaxin binding / peroxisomal membrane / regulation of synaptic vesicle endocytosis / clathrin binding / regulation of dopamine secretion / phosphatidylserine binding / regulation of insulin secretion / GABA-ergic synapse / phagocytosis / axon terminus / phosphatidylinositol-4,5-bisphosphate binding / cellular response to calcium ion / hippocampal mossy fiber to CA3 synapse / SNARE binding / synaptic vesicle membrane / phagocytic vesicle membrane / synaptic vesicle / peroxisome / presynaptic membrane / lysosome / calmodulin binding / axon / lysosomal membrane / neuronal cell body / glutamatergic synapse / synapse / dendrite / 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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.441 Å
AuthorsTomchick, D.R. / Rizo, J. / Craig, T.K.
CitationJournal: 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
DepositionMay 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)16,1165
Polymers15,9561
Non-polymers1604
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.598, 44.892, 87.383
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 15955.729 Da / Num. of mol.: 1 / Fragment: C2B domain residues 266-403
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Syt7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9R0N7
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.19 Å3/Da / Density % sol: 43.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 3350, 0.2 M Li2SO4, 0.1 M Hepes pH 6.5, 0.05 M NaCl, 0.02 M CaCl2, 1 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0148 Å
DetectorType: SBC-3 / Detector: CCD / Date: Apr 10, 2009 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0148 Å / Relative weight: 1
ReflectionResolution: 1.44→43.7 Å / Num. all: 25581 / Num. obs: 25581 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 31.1
Reflection shellResolution: 1.44→1.46 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1158 / % possible all: 91

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Processing

Software
NameVersionClassificationNB
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TJM

1tjm


Resolution: 1.441→23.51 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.909 / SU ML: 0.14 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 15.01 / Stereochemistry target values: ML / Details: Hydrogens were added in the riding positions.
RfactorNum. reflection% reflectionSelection details
Rfree0.181 1310 5.13 %RANDOM
Rwork0.16 ---
all0.161 25550 --
obs0.161 25550 98.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.201 Å2 / ksol: 0.505 e/Å3
Displacement parametersBiso max: 82.1 Å2 / Biso mean: 17.529 Å2 / Biso min: 2.66 Å2
Baniso -1Baniso -2Baniso -3
1-2.968 Å20 Å2-0 Å2
2--0.013 Å20 Å2
3----2.98 Å2
Refine analyzeLuzzati sigma a obs: 0.14 Å
Refinement stepCycle: LAST / Resolution: 1.441→23.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1120 0 4 183 1307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0211300
X-RAY DIFFRACTIONf_angle_d1.341788
X-RAY DIFFRACTIONf_chiral_restr0.083190
X-RAY DIFFRACTIONf_plane_restr0.008224
X-RAY DIFFRACTIONf_dihedral_angle_d14.753504
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.441-1.4990.241430.19325382681268194
1.499-1.5670.2111460.16226152761276198
1.567-1.6490.1821480.14926412789278998
1.649-1.7530.1661290.13726772806280698
1.753-1.8880.151440.13426942838283899
1.888-2.0780.1371450.12426842829282999
2.078-2.3780.1331550.13527432898289899
2.378-2.9950.1981430.15527692912291299
2.995-23.5130.1931570.17728793036303699
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)
10.47850.0960.3608-0.0046-0.02430.2145-0.01970.07950.0044-0.0101-0.02380.0052-0.12620.0346-0.00910.0781-0.00450.00810.0770.01080.071411.370229.196-11.2147
20.0214-0.0498-0.01150.02810.03460.07-0.0202-0.0405-0.00030.03210.07630.0453-0.0256-0.03020.01540.07240.00230.00470.07050.0110.086110.578523.6067.1135
30.0738-0.1107-0.04860.09070.04670.0282-0.02280.0152-0.04820.02830.0478-0.03220.10.10470.00050.09410.00770.00040.08330.00410.079516.25119.60776.7458
40.1203-0.01810.0050.04680.02360.0340.01320.1681-0.3491-0.09060.1551-0.12510.19770.32180.00240.1169-0.0005-0.00360.1365-0.03540.120314.407714.6007-15.0478
50.1067-0.08750.00530.07930.0860.0707-0.00270.1431-0.00590.17640.0211-0.10610.28770.0347-0.00570.0896-0.0116-0.01520.1309-0.00030.091120.734223.09243.3086
60.2158-0.15640.08860.1171-0.03220.0391-0.01340.0770.00090.02290.0071-0.00520.0007-0.0005-00.063-0.0117-0.00360.0729-0.00140.068717.07429.1714-1.3286
70.0058-0.00850.0021-0.00030.00430.0111-0.0321-0.07960.1088-0.12810.1713-0.05050.12290.40370.00020.1374-0.0031-0.01890.1693-0.01840.098713.419623.7213-23.7959
80.00680.01640.00230.0117-0.0040.04740.08960.13470.0944-0.2382-0.06020.2938-0.1532-0.33930.00390.1260.0157-0.04240.16090.0070.08666.781919.6766-20.4436
9-0.02130.03060.03040.0356-0.03010.0389-0.01730.0976-0.089-0.0214-0.0059-0.07390.0530.1132-0.00290.09410.0056-0.00610.07680.00490.096314.753917.83840.3216
100.07110.0009-0.06460.0502-0.0550.0570.080.1075-0.0749-0.0625-0.0196-0.01160.17880.0449-0.00090.09110.0138-0.01280.07950.00120.105616.495311.86385.4772
110.0839-0.025-0.02230.09410.04460.01570.1463-0.1454-0.154-0.06860.01210.06710.192-0.13750.00930.0718-0.0111-0.01740.10980.00870.12311.832821.5448-11.0104
120.93020.043-0.3370.1189-0.15570.34030.016-0.0664-0.182-0.0927-0.15090.137-0.2252-0.0751-0.0120.05930.0293-0.00340.0403-0.01740.05623.214131.2907-15.3215
130.21040.17050.01951.29430.08470.3523-0.07580.0405-0.0058-0.11080.15810.18490.0084-0.2203-0.16120.0235-0.00590.00020.0310.01120.04435.755530.4758-6.3074
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 266:286)A266 - 286
2X-RAY DIFFRACTION2(chain A and resid 287:297)A287 - 297
3X-RAY DIFFRACTION3(chain A and resid 298:308)A298 - 308
4X-RAY DIFFRACTION4(chain A and resid 309:318)A309 - 318
5X-RAY DIFFRACTION5(chain A and resid 319:328)A319 - 328
6X-RAY DIFFRACTION6(chain A and resid 329:339)A329 - 339
7X-RAY DIFFRACTION7(chain A and resid 340:345)A340 - 345
8X-RAY DIFFRACTION8(chain A and resid 346:350)A346 - 350
9X-RAY DIFFRACTION9(chain A and resid 351:359)A351 - 359
10X-RAY DIFFRACTION10(chain A and resid 360:369)A360 - 369
11X-RAY DIFFRACTION11(chain A and resid 370:381)A370 - 381
12X-RAY DIFFRACTION12(chain A and resid 382:391)A382 - 391
13X-RAY DIFFRACTION13(chain A and resid 392:403)A392 - 403

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