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- PDB-1dqv: CRYSTAL STRUCTURE OF SYNAPTOTAGMIN III C2A/C2B -

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Basic information

Entry
Database: PDB / ID: 1dqv
TitleCRYSTAL STRUCTURE OF SYNAPTOTAGMIN III C2A/C2B
ComponentsSYNAPTOTAGMIN III
KeywordsENDOCYTOSIS/EXOCYTOSIS / beta sandwich / calcium ion / C2 domain / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


positive regulation of vesicle fusion / regulation of calcium ion-dependent exocytosis / calcium ion sensor activity / exocytic vesicle / positive regulation of dendrite extension / calcium-ion regulated exocytosis / calcium-dependent phospholipid binding / syntaxin binding / clathrin binding / transport vesicle membrane ...positive regulation of vesicle fusion / regulation of calcium ion-dependent exocytosis / calcium ion sensor activity / exocytic vesicle / positive regulation of dendrite extension / calcium-ion regulated exocytosis / calcium-dependent phospholipid binding / syntaxin binding / clathrin binding / transport vesicle membrane / phosphatidylserine binding / synaptic vesicle exocytosis / regulation of postsynaptic membrane neurotransmitter receptor levels / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / synaptic membrane / SNARE binding / response to calcium ion / presynapse / chemical synaptic transmission / cell differentiation / postsynapse / protein heterodimerization activity / calcium ion binding / protein homodimerization activity / identical protein binding / plasma membrane
Similarity search - Function
Synaptotagmin / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesRattus rattus (black rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsSutton, R.B. / Ernst, J.A. / Brunger, A.T.
CitationJournal: J.Cell Biol. / Year: 1999
Title: Crystal structure of the cytosolic C2A-C2B domains of synaptotagmin III. Implications for Ca(+2)-independent snare complex interaction.
Authors: Sutton, R.B. / Ernst, J.A. / Brunger, A.T.
History
DepositionJan 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
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_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 III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4476
Polymers33,2541
Non-polymers1935
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: SYNAPTOTAGMIN III
hetero molecules

A: SYNAPTOTAGMIN III
hetero molecules

A: SYNAPTOTAGMIN III
hetero molecules

A: SYNAPTOTAGMIN III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,78924
Polymers133,0164
Non-polymers77320
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_765-x+2,-y+1,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+1/31
crystal symmetry operation12_555x,x-y,-z+1/31
Buried area9750 Å2
ΔGint-160 kcal/mol
Surface area53210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.959, 125.959, 118.438
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
DetailsThe biological assembly is one C2A domain and one C2B domain

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Components

#1: Protein SYNAPTOTAGMIN III


Mass: 33253.914 Da / Num. of mol.: 1 / Fragment: C2A/C2B
Source method: isolated from a genetically manipulated source
Details: SOLUBLE PORTION / Source: (gene. exp.) Rattus rattus (black rat) / Organ: BRAIN / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / References: UniProt: P40748
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 11

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Sample preparation

CrystalDensity Matthews: 4.08 Å3/Da / Density % sol: 69.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M Magnesium Sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mg/mlprotein1drop
21.5 M1reservoirMgCl2
3100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 13, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 61080 / Num. obs: 9578 / % possible obs: 99.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.3 % / Biso Wilson estimate: -1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 2.9
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 7 % / Rmerge(I) obs: 0.785 / Num. unique all: 929 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 61080
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 3.2→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: used maximum likelihood/experiment phase set target function
RfactorNum. reflection% reflectionSelection details
Rfree0.3485 1564 -random
Rwork0.293 ---
all0.293 16371 --
obs0.293 16371 94.3 %-
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2186 0 9 0 2195
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.622
X-RAY DIFFRACTIONc_bond_d0.0084
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.349
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.62
LS refinement shell
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 3.45 Å / Rfactor Rfree: 0.344 / Rfactor Rwork: 0.302

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