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- PDB-4v11: Structure of Synaptotagmin-1 with SV2A peptide phosphorylated at Thr84 -

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Basic information

Entry
Database: PDB / ID: 4v11
TitleStructure of Synaptotagmin-1 with SV2A peptide phosphorylated at Thr84
Components
  • SYNAPTIC VESICLE GLYCOPROTEIN 2A
  • SYNAPTOTAGMIN-1
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


regulation of gamma-aminobutyric acid secretion / clathrin-sculpted acetylcholine transport vesicle membrane / clathrin-sculpted glutamate transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / Toxicity of botulinum toxin type F (botF) / Toxicity of botulinum toxin type D (botD) / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / Toxicity of botulinum toxin type E (botE) ...regulation of gamma-aminobutyric acid secretion / clathrin-sculpted acetylcholine transport vesicle membrane / clathrin-sculpted glutamate transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / Toxicity of botulinum toxin type F (botF) / Toxicity of botulinum toxin type D (botD) / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / Toxicity of botulinum toxin type E (botE) / syntaxin-3 binding / calcium-dependent activation of synaptic vesicle fusion / Acetylcholine Neurotransmitter Release Cycle / Toxicity of botulinum toxin type A (botA) / regulation of regulated secretory pathway / calcium ion sensor activity / clathrin-sculpted monoamine transport vesicle membrane / Toxicity of botulinum toxin type B (botB) / spontaneous neurotransmitter secretion / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Serotonin Neurotransmitter Release Cycle / dense core granule / chromaffin granule membrane / GABA synthesis, release, reuptake and degradation / calcium ion-regulated exocytosis of neurotransmitter / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / vesicle docking / regulation of calcium ion-dependent exocytosis / exocytic vesicle / positive regulation of dopamine secretion / protein heterooligomerization / Glutamate Neurotransmitter Release Cycle / regulation of exocytosis / neurotransmitter secretion / positive regulation of dendrite extension / calcium-dependent phospholipid binding / neuron projection terminus / Neurexins and neuroligins / syntaxin-1 binding / syntaxin binding / synaptic vesicle priming / clathrin binding / low-density lipoprotein particle receptor binding / phosphatidylserine binding / regulation of dopamine secretion / presynaptic active zone / excitatory synapse / transmembrane transporter activity / synaptic vesicle endocytosis / detection of calcium ion / GABA-ergic synapse / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / phosphatidylinositol-4,5-bisphosphate binding / cellular response to calcium ion / hippocampal mossy fiber to CA3 synapse / SNARE binding / clathrin-coated endocytic vesicle membrane / neuromuscular junction / synaptic vesicle membrane / intracellular calcium ion homeostasis / calcium-dependent protein binding / cell-cell junction / synaptic vesicle / Cargo recognition for clathrin-mediated endocytosis / presynaptic membrane / Clathrin-mediated endocytosis / chemical synaptic transmission / cell differentiation / calmodulin binding / neuron projection / protein heterodimerization activity / axon / neuronal cell body / glutamatergic synapse / dendrite / calcium ion binding / protein kinase binding / Golgi apparatus / endoplasmic reticulum / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Synaptic vesicle protein SV2 / Synaptotagmin / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Sugar transporter, conserved site / Major facilitator superfamily / Major Facilitator Superfamily / C2 domain / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. ...Synaptic vesicle protein SV2 / Synaptotagmin / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Sugar transporter, conserved site / Major facilitator superfamily / Major Facilitator Superfamily / C2 domain / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / MFS transporter superfamily / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Synaptotagmin-1 / Synaptic vesicle glycoprotein 2A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsZhang, N. / Gordon, S.L. / Fritsch, M.J. / Esoof, N. / Campbell, D. / Gourlay, R. / Velupillai, S. / Macartney, T. / Peggie, M. / vanAalten, D.M.F. ...Zhang, N. / Gordon, S.L. / Fritsch, M.J. / Esoof, N. / Campbell, D. / Gourlay, R. / Velupillai, S. / Macartney, T. / Peggie, M. / vanAalten, D.M.F. / Cousin, M.A. / Alessi, D.R.
CitationJournal: J.Neurosci. / Year: 2015
Title: Phosphorylation of Synaptic Vesicle Protein 2A at Thr84 by Casein Kinase 1 Family Kinases Controls the Specific Retrieval of Synaptotagmin-1.
Authors: Zhang, N. / Gordon, S.L. / Fritsch, M.J. / Esoof, N. / Campbell, D.G. / Gourlay, R. / Velupillai, S. / Macartney, T. / Peggie, M. / Van Aalten, D.M.F. / Cousin, M.A. / Alessi, D.R.
History
DepositionSep 22, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.2Jan 10, 2024Group: 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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.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-1
B: SYNAPTIC VESICLE GLYCOPROTEIN 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4636
Polymers18,2512
Non-polymers2124
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-40.1 kcal/mol
Surface area8710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.049, 41.432, 48.014
Angle α, β, γ (deg.)90.00, 96.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 17094.957 Da / Num. of mol.: 1 / Fragment: C2B DOMAIN, UNP RESIDUES 273-422
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P-1 TEVB SYT1 270-END / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21579
#2: Protein/peptide SYNAPTIC VESICLE GLYCOPROTEIN 2A / SV2A


Mass: 1155.944 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 81-90 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q7L0J3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 81-90 WITH PHOSPHORYLATED T84

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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: 2.71 Å3/Da / Density % sol: 54.71 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M HEPES PH 7.5, 18 % PEG 3350, 0.05 M CACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178
DetectorType: RIGAKU SATURN 994 CCD-DETECTOR / Detector: CCD / Date: Mar 17, 2014 / Details: VARIMAX CU-VHF OPTICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.95→31.28 Å / Num. obs: 13172 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 10.04 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 58.93
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.03 / Mean I/σ(I) obs: 23.39 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXPHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TJX

1tjx


Resolution: 1.95→31.279 Å / SU ML: 0.16 / σ(F): 1.38 / Phase error: 17.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1956 687 5.2 %
Rwork0.1512 --
obs0.1534 13172 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.9 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 11 Å2
Refinement stepCycle: LAST / Resolution: 1.95→31.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1281 0 9 147 1437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071315
X-RAY DIFFRACTIONf_angle_d1.0041774
X-RAY DIFFRACTIONf_dihedral_angle_d13.146502
X-RAY DIFFRACTIONf_chiral_restr0.046198
X-RAY DIFFRACTIONf_plane_restr0.004224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.10060.19381270.12912383X-RAY DIFFRACTION95
2.1006-2.31190.22111610.14322480X-RAY DIFFRACTION100
2.3119-2.64630.18091300.15932502X-RAY DIFFRACTION100
2.6463-3.33340.21581380.15922525X-RAY DIFFRACTION100
3.3334-31.28260.17421310.15392595X-RAY DIFFRACTION100

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