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- PDB-3hn8: Crystal structure of synaptotagmin -

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Basic information

Entry
Database: PDB / ID: 3hn8
TitleCrystal structure of synaptotagmin
ComponentsSynaptotagmin-3
KeywordsSIGNALING PROTEIN / synaptotagmin / Cell junction / Cytoplasmic vesicle / Membrane / Metal-binding / Synapse / Transmembrane
Function / homology
Function and homology information


positive regulation of vesicle fusion / regulation of calcium ion-dependent exocytosis / exocytic vesicle / calcium-ion regulated exocytosis / positive regulation of dendrite extension / calcium-dependent phospholipid binding / syntaxin binding / transport vesicle membrane / clathrin binding / regulation of dopamine secretion ...positive regulation of vesicle fusion / regulation of calcium ion-dependent exocytosis / exocytic vesicle / calcium-ion regulated exocytosis / positive regulation of dendrite extension / calcium-dependent phospholipid binding / syntaxin binding / transport vesicle membrane / clathrin binding / regulation of dopamine secretion / phosphatidylserine binding / synaptic vesicle exocytosis / phosphatidylinositol-4,5-bisphosphate binding / cellular response to calcium ion / SNARE binding / synaptic membrane / response to calcium ion / presynapse / cell differentiation / protein heterodimerization activity / calcium ion binding / protein homodimerization activity / identical protein binding / plasma membrane
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
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsStrop, P. / Vrljic, M. / Ernst, J. / Brunger, A.T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Molecular mechanism of the synaptotagmin-SNARE interaction in Ca2+-triggered vesicle fusion.
Authors: Vrljic, M. / Strop, P. / Ernst, J.A. / Sutton, R.B. / Chu, S. / Brunger, A.T.
History
DepositionMay 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Synaptotagmin-3
B: Synaptotagmin-3
C: Synaptotagmin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,46324
Polymers99,5463
Non-polymers91821
Water0
1
A: Synaptotagmin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4888
Polymers33,1821
Non-polymers3067
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Synaptotagmin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4888
Polymers33,1821
Non-polymers3067
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Synaptotagmin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4888
Polymers33,1821
Non-polymers3067
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)205.675, 205.675, 143.125
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 295:412 or resseq 414:573 )A295 - 412
121chain A and (resseq 295:412 or resseq 414:573 )A414 - 573
211chain B and (resseq 295:412 or resseq 414:573 )B295 - 412
221chain B and (resseq 295:412 or resseq 414:573 )B414 - 573
311chain C and (resseq 295:412 or resseq 414:573 )C295 - 412
321chain C and (resseq 295:412 or resseq 414:573 )C414 - 573

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.044483, 0.998188, 0.040528), (-0.052226, -0.042836, 0.997716), (0.997644, 0.042265, 0.054037)-146.026001, 35.2094, 101.112999
3given(-0.071986, 0.014386, 0.997302), (-0.001424, -0.999896, 0.014321), (0.997405, -0.000389, 0.071999)-72.120499, 39.933399, 66.350899

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Components

#1: Protein Synaptotagmin-3 / / Synaptotagmin III / SytIII


Mass: 33181.852 Da / Num. of mol.: 3 / Fragment: UNP residues 292-587
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Syt3 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40748
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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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: 7.6 Å3/Da / Density % sol: 83.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 17% MPD, 50mM CaCl2, 100mM NaCl, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9778 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 22, 2000
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionRedundancy: 5.8 % / Av σ(I) over netI: 10.36 / Number: 228916 / Rmerge(I) obs: 0.167 / Χ2: 1.25 / D res high: 3.5 Å / D res low: 50 Å / Num. obs: 39136 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.535097.610.0440.9815.5
5.987.5399.810.1071.1555.9
5.235.9899.910.1431.1725.9
4.755.2399.910.1411.1826
4.414.7510010.1541.1846
4.154.4199.910.1981.2856
3.944.1510010.2961.3776
3.773.9499.810.4251.5885.5
3.633.7710010.4971.0555.8
3.53.6310010.5711.5895.9
ReflectionResolution: 3.5→50 Å / Num. all: 39136 / Num. obs: 39136 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.167 / Χ2: 1.255 / Net I/σ(I): 10.361
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.571 / Num. unique all: 3851 / Χ2: 1.589 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→29.816 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.802 / SU ML: -0 / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.259 3927 10.06 %random
Rwork0.238 ---
all0.24 39055 --
obs0.24 39055 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.648 Å2 / ksol: 0.308 e/Å3
Displacement parametersBiso max: 257.56 Å2 / Biso mean: 90.786 Å2 / Biso min: 35.38 Å2
Baniso -1Baniso -2Baniso -3
1--20.984 Å2-0 Å20 Å2
2---20.984 Å2-0 Å2
3---41.969 Å2
Refinement stepCycle: LAST / Resolution: 3.5→29.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6651 0 21 0 6672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046806
X-RAY DIFFRACTIONf_angle_d0.9379228
X-RAY DIFFRACTIONf_chiral_restr0.0641029
X-RAY DIFFRACTIONf_plane_restr0.0051197
X-RAY DIFFRACTIONf_dihedral_angle_d25.1634197
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2209X-RAY DIFFRACTIONPOSITIONAL0.017
12B2209X-RAY DIFFRACTIONPOSITIONAL0.017
13C2209X-RAY DIFFRACTIONPOSITIONAL0.022
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.5430.3421400.3191235137599
3.543-3.5880.3311460.3112121358100
3.588-3.6350.3421370.29512581395100
3.635-3.6850.331370.30112291366100
3.685-3.7370.3221390.29412321371100
3.737-3.7930.3431260.30112421368100
3.793-3.8520.2861480.28312191367100
3.852-3.9150.2671400.2731234137499
3.915-3.9820.3061220.28112611383100
3.982-4.0550.2881460.25412231369100
4.055-4.1320.2461560.2512161372100
4.132-4.2160.2631400.22212571397100
4.216-4.3080.2311440.22512331377100
4.308-4.4080.2351490.19812431392100
4.408-4.5180.1931390.18812341373100
4.518-4.6390.1911430.18512641407100
4.639-4.7750.1811130.17212611374100
4.775-4.9290.1831180.19312841402100
4.929-5.1040.2161420.1912481390100
5.104-5.3070.1871560.20412431399100
5.307-5.5480.2841160.22812741390100
5.548-5.8380.2951440.24412611405100
5.838-6.2010.3161490.24712611410100
6.201-6.6740.2371230.25412991422100
6.674-7.3370.2981590.23512641423100
7.337-8.3780.2291580.21512751433100
8.378-10.4790.1991290.17713311460100
10.479-29.8170.2781680.2841335150398
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)
10.499-0.564-0.58760.88630.60160.9494-0.07230.24820.0089-0.038-0.2014-0.04240.0006-0.16250.20810.61860.11910.05350.6825-0.14970.5171-61.809840.36550.5193
21.08660.1043-0.4061.195-0.12370.40660.1150.2457-0.64790.1358-0.1166-0.3335-0.0376-0.07190.02540.446-0.05140.14770.4974-0.19210.7234-64.361536.686724.8559
3-0.593-0.07451.08071.4073-0.34241.43480.07560.0560.2117-0.0753-0.42330.76990.0556-0.1790.20830.43020.0186-0.04080.7950.0230.7967-104.374479.59313.1155
40.81140.28030.25971.17350.952-0.2017-0.04940.1291-0.1039-0.3457-0.0826-0.0672-0.28540.13190.1660.53890.1090.00350.56080.00520.333-79.786978.22960.663
51.4511-0.37610.04370.74510.62221.12930.1927-0.10490.1268-0.00520.0420.13870.06490.0423-0.14340.53140.0368-0.08070.5235-0.22680.828-66.3983-0.2265.5432
60.4444-0.09130.22720.6685-0.46660.21550.08860.0651-0.24020.21420.053-0.2398-0.1430.029-0.14770.59090.08540.02660.5328-0.20740.6394-41.94183.37364.7038
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 295:427A295 - 427
2X-RAY DIFFRACTION2chain A and resid 428:573A428 - 573
3X-RAY DIFFRACTION3chain B and resid 295:427B295 - 427
4X-RAY DIFFRACTION4chain B and resid 428:573B428 - 573
5X-RAY DIFFRACTION5chain C and resid 295:427C295 - 427
6X-RAY DIFFRACTION6chain C and resid 428:573C428 - 573

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