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- PDB-2yoa: Synaptotagmin-1 C2B domain with phosphoserine -

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Basic information

Entry
Database: PDB / ID: 2yoa
TitleSynaptotagmin-1 C2B domain with phosphoserine
ComponentsSYNAPTOTAGMIN-1
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / calcium-dependent activation of synaptic vesicle fusion / regulation of regulated secretory pathway / calcium ion sensor activity / spontaneous neurotransmitter secretion / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle ...synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / calcium-dependent activation of synaptic vesicle fusion / regulation of regulated secretory pathway / calcium ion sensor activity / spontaneous neurotransmitter secretion / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / dense core granule / GABA synthesis, release, reuptake and degradation / positive regulation of vesicle fusion / chromaffin granule membrane / Dopamine Neurotransmitter Release Cycle / calcium ion-regulated exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis / vesicle docking / regulation of calcium ion-dependent exocytosis / exocytic vesicle / positive regulation of dopamine secretion / protein heterooligomerization / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / calcium-ion regulated exocytosis / neurotransmitter secretion / positive regulation of dendrite extension / neuron projection terminus / calcium-dependent phospholipid binding / syntaxin-1 binding / low-density lipoprotein particle receptor binding / syntaxin binding / regulation of synaptic vesicle exocytosis / clathrin binding / phosphatidylserine binding / regulation of dopamine secretion / synaptic vesicle exocytosis / excitatory synapse / synaptic vesicle endocytosis / detection of calcium ion / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / phosphatidylinositol-4,5-bisphosphate binding / hippocampal mossy fiber to CA3 synapse / cellular response to calcium ion / SNARE binding / secretory granule / phospholipid binding / terminal bouton / synaptic vesicle membrane / response to calcium ion / calcium-dependent protein binding / synaptic vesicle / presynaptic membrane / cell differentiation / calmodulin binding / neuron projection / protein heterodimerization activity / axon / glutamatergic synapse / calcium ion binding / Golgi apparatus / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
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
THIOCYANATE ION / PHOSPHOSERINE / Synaptotagmin-1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHonigmann, A. / van den Bogaart, G. / Iraheta, E. / Risselada, H.J. / Milovanovic, D. / Mueller, V. / Muellar, S. / Diederichsen, U. / Fasshauer, D. / Grubmuller, H. ...Honigmann, A. / van den Bogaart, G. / Iraheta, E. / Risselada, H.J. / Milovanovic, D. / Mueller, V. / Muellar, S. / Diederichsen, U. / Fasshauer, D. / Grubmuller, H. / Hell, S.W. / Eggeling, C. / Kuhnel, K. / Jahn, R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Phosphatidylinositol 4,5-Bisphosphate Clusters Act as Molecular Beacons for Vesicle Recruitment
Authors: Honigmann, A. / Van Den Bogaart, G. / Iraheta, E. / Risselada, H.J. / Milovanovic, D. / Mueller, V. / Muellar, S. / Diederichsen, U. / Fasshauer, D. / Grubmuller, H. / Hell, S.W. / Eggeling, ...Authors: Honigmann, A. / Van Den Bogaart, G. / Iraheta, E. / Risselada, H.J. / Milovanovic, D. / Mueller, V. / Muellar, S. / Diederichsen, U. / Fasshauer, D. / Grubmuller, H. / Hell, S.W. / Eggeling, C. / Kuhnel, K. / Jahn, R.
History
DepositionOct 22, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2May 29, 2013Group: Database references
Revision 1.3Jun 19, 2013Group: Database references
Revision 1.4Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.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

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Assembly

Deposited unit
A: SYNAPTOTAGMIN-1
B: SYNAPTOTAGMIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,65216
Polymers34,7112
Non-polymers94114
Water4,612256
1
A: SYNAPTOTAGMIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8178
Polymers17,3551
Non-polymers4627
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SYNAPTOTAGMIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8358
Polymers17,3551
Non-polymers4807
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.000, 97.000, 89.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-2102-

HOH

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Components

#1: Protein SYNAPTOTAGMIN-1 / / SYNAPTOTAGMIN I / SYTI / P65


Mass: 17355.268 Da / Num. of mol.: 2 / Fragment: C2B DOMAIN, RESIDUES 271-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21707
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SEP / PHOSPHOSERINE / PHOSPHONOSERINE / Phosphoserine


Type: L-peptide linking / Mass: 185.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8NO6P
#4: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CNS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 3 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growDetails: 0.2 M KSCN, 20 % PEG 600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 66840 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 12.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 43.9
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 7.9 / % possible all: 81.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UOV

1uov


Resolution: 1.5→44.5 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.743 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20404 3342 5 %RANDOM
Rwork0.18255 ---
obs0.18361 63497 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.492 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.5→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2385 0 44 256 2685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222517
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.9763363
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.055304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.95625.094106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87515.063476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9561510
X-RAY DIFFRACTIONr_chiral_restr0.0830.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021812
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2520.21105
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21725
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0980.2167
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0940.211
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4810.288
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0830.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9611.51550
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.58422472
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4483967
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7114.5891
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.46732517
X-RAY DIFFRACTIONr_sphericity_free4.2773260
X-RAY DIFFRACTIONr_sphericity_bonded2.89832456
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 203 -
Rwork0.171 3865 -
obs--100 %

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