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- PDB-1w16: rat synaptotagmin 4 C2B domain in the absence of calcium -

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Basic information

Entry
Database: PDB / ID: 1w16
Titlerat synaptotagmin 4 C2B domain in the absence of calcium
ComponentsSYNAPTOTAGMIN IV
KeywordsMETAL BINDING PROTEIN / SYNAPTOTAGMIN / ENDOCYTOSIS/EXOCYTOSIS / NEUROTRANSMITTER RELEASE / TRANSMEMBRANE
Function / homology
Function and homology information


vesicle fusion with vesicle / secretory granule maturation / negative regulation of dense core granule exocytosis / negative regulation of short-term neuronal synaptic plasticity / regulation of trans-synaptic signaling by BDNF, modulating synaptic transmission / regulation of postsynaptic dense core vesicle exocytosis / positive regulation of dense core granule exocytosis / negative regulation of retrograde trans-synaptic signaling by neuropeptide / negative regulation of vesicle fusion / negative regulation of catecholamine secretion ...vesicle fusion with vesicle / secretory granule maturation / negative regulation of dense core granule exocytosis / negative regulation of short-term neuronal synaptic plasticity / regulation of trans-synaptic signaling by BDNF, modulating synaptic transmission / regulation of postsynaptic dense core vesicle exocytosis / positive regulation of dense core granule exocytosis / negative regulation of retrograde trans-synaptic signaling by neuropeptide / negative regulation of vesicle fusion / negative regulation of catecholamine secretion / regulation of vesicle fusion / microvesicle / syntaxin-3 binding / neuronal dense core vesicle membrane / dense core granule cytoskeletal transport / dense core granule / regulation of calcium ion-dependent exocytosis / calcium ion-regulated exocytosis of neurotransmitter / vesicle fusion / negative regulation of neurotransmitter secretion / exocytic vesicle / negative regulation of calcium ion-dependent exocytosis / negative regulation of synaptic vesicle exocytosis / calcium-ion regulated exocytosis / positive regulation of dendrite extension / astrocyte projection / neurotransmitter secretion / positive regulation of glutamate secretion / calcium-dependent phospholipid binding / neuron projection terminus / syntaxin binding / syntaxin-1 binding / clathrin binding / regulation of dopamine secretion / phosphatidylserine binding / neuronal dense core vesicle / regulation of endocytosis / negative regulation of protein secretion / somatodendritic compartment / SNARE binding / secretory granule membrane / memory / synaptic vesicle / vesicle / cell differentiation / neuron projection / protein heterodimerization activity / axon / neuronal cell body / glutamatergic synapse / dendrite / calcium ion binding / synapse / perinuclear region of cytoplasm / Golgi apparatus / protein homodimerization activity / membrane / 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 NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDai, H. / Shin, O.-H. / Machius, M. / Tomchick, D.R. / Sudhof, T.C. / Rizo, J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structural Basis for the Evolutionary Inactivation of Ca2+ Binding to Synaptotagmin 4
Authors: Dai, H. / Shin, O.-H. / Machius, M. / Tomchick, D.R. / Sudhof, T.C. / Rizo, J.
History
DepositionJun 16, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 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
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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SYNAPTOTAGMIN IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,91410
Polymers16,6201
Non-polymers2949
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.061, 91.061, 122.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-3001-

CL

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Components

#1: Protein SYNAPTOTAGMIN IV


Mass: 16620.102 Da / Num. of mol.: 1 / Fragment: C2B DOMAIN, RESIDUES 288-425
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PGEX-KG / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P50232
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMAY BE INVOLVED IN CA(2+)-DEPENDENT EXOCYTOSIS OF SECRETORY VESICLES THROUGH CA(2+)

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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: 4.4 Å3/Da / Density % sol: 72 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: THE RAT SYNAPTOTAGMIN IV C2B DOMAIN WAS CRYSTALLIZED BY THE VAPOR DIFFUSION METHOD (HANGING DROP) BY MIXING 1 MICROLITER PROTEIN (IN 20 MM MES, 150 MM NACL AND 1 MM EDTA, PH 6.32) WITH 1 ...Details: THE RAT SYNAPTOTAGMIN IV C2B DOMAIN WAS CRYSTALLIZED BY THE VAPOR DIFFUSION METHOD (HANGING DROP) BY MIXING 1 MICROLITER PROTEIN (IN 20 MM MES, 150 MM NACL AND 1 MM EDTA, PH 6.32) WITH 1 MICROLITER RESERVOIR SOLUTION (2.5M NACL, 0.1M CACL2, 0.1M HEPES, PH 7.5) SUSPENDED OVER 500 MICROLITERS RESERVOIR SOLUTION. HEXAGONAL CRYSTALS APPEARED OVERNIGHT AND GREW TO A FINAL SIZE OF 0.1 X 0.1 X 0.2 MM WITHIN TWO DAYS. PRIOR TO DATA COLLECTION, CRYSTALS WERE TRANSFERRED INTO CRYSTALLIZATION SOLUTION CONTAINING 4.25 M NACL, 0.1 M HEPES PH 7.5 AND 5%(V/V) ETHYLENE GLYCOL AND THEN COOLED IN LIQUID PROPANE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9876
DetectorType: CUSTOM / Detector: CCD / Date: Nov 29, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9876 Å / Relative weight: 1
ReflectionResolution: 2.3→29.81 Å / Num. obs: 13974 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 45.8
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 1.8 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K5W

1k5w


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.453 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1392 10 %RANDOM
Rwork0.213 ---
obs0.217 12558 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 55.09 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20.51 Å20 Å2
2--1.02 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 9 53 1054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0211027
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.9491388
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4235126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55722.95544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.58315186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.413158
X-RAY DIFFRACTIONr_chiral_restr0.1150.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02757
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.2410
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2662
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.259
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0530.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2161.5630
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.24721021
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1143410
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8154.5367
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 105 -
Rwork0.32 850 -
obs--94.93 %
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)
15.7711-1.1001-5.40136.1312-3.204612.2066-0.58550.1261-0.353-0.2010.1407-0.08260.98790.02560.4448-0.024-0.0319-0.0061-0.130.0285-0.042541.26915.524946.4235
24.2746-1.7174-2.42236.4880.77247.193-0.1873-0.34150.18870.93670.33910.21760.2883-0.2718-0.15180.0177-0.00230.0296-0.12110.0764-0.06938.608513.445258.2845
31.92440.1112-0.70953.5619-3.26314.8817-0.14590.08-0.11690.04980.0735-0.020.5197-0.02440.07240.0355-0.004-0.0022-0.17870.0182-0.09343.38259.011450.8988
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A273 - 300
2X-RAY DIFFRACTION2A308 - 331
3X-RAY DIFFRACTION3A336 - 409

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