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- PDB-8faf: Unedited Octopus bimaculoides Synaptotagmin 1 C2A at room temperature -

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Basic information

Entry
Database: PDB / ID: 8faf
TitleUnedited Octopus bimaculoides Synaptotagmin 1 C2A at room temperature
ComponentsSynaptotagmin
KeywordsEXOCYTOSIS / synaptotagmin 1 / C2 domain / RNA-editing
Function / homology
Function and homology information


calcium ion-regulated exocytosis of neurotransmitter / dense core granule / calcium-dependent phospholipid binding / clathrin binding / phosphatidylserine binding / synaptic vesicle endocytosis / SNARE binding / synaptic vesicle membrane / axon / calcium ion binding / plasma membrane
Similarity search - Function
Synaptotagmin / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
C2 domain-containing protein
Similarity search - Component
Biological speciesOctopus bimaculoides (California two-spot octopus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMcNeme, S. / Dominguez, M.J. / Birk, M.A. / Rosenthal, J.C. / Sutton, R.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2023
Title: Temperature-dependent RNA editing in octopus extensively recodes the neural proteome.
Authors: Birk, M.A. / Liscovitch-Brauer, N. / Dominguez, M.J. / McNeme, S. / Yue, Y. / Hoff, J.D. / Twersky, I. / Verhey, K.J. / Sutton, R.B. / Eisenberg, E. / Rosenthal, J.J.C.
History
DepositionNov 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Synaptotagmin


Theoretical massNumber of molelcules
Total (without water)15,5931
Polymers15,5931
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.728, 54.940, 84.143
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Synaptotagmin


Mass: 15592.720 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Octopus bimaculoides (California two-spot octopus)
Gene: OCBIM_22021175mg / Plasmid: p202 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0L8IHK9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.13 Å3/Da / Density % sol: 42.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 23% PEG 3350, 100 mM CHES

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→42.07 Å / Num. obs: 20317 / % possible obs: 82.99 % / Redundancy: 3.2 % / CC1/2: 0.995 / CC star: 0.999 / Net I/σ(I): 7.1
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.6201 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2009 / CC1/2: 0.632 / CC star: 0.88 / % possible all: 41.26

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Processing

Software
NameVersionClassification
PHENIX1.20,1-4487-000refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→42.07 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2237 1155 10 %
Rwork0.1807 --
obs0.185 11549 96.12 %
Refinement stepCycle: LAST / Resolution: 1.85→42.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1035 0 0 32 1067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.809
X-RAY DIFFRACTIONf_dihedral_angle_d9.425139
X-RAY DIFFRACTIONf_chiral_restr0.055156
X-RAY DIFFRACTIONf_plane_restr0.005188
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)
10.49340.34140.60193.19043.29754.4139-0.0432-0.04310.1063-0.0084-0.01720.0021-0.2412-0.16880.01170.27940.02850.0270.24560.00370.2619-0.33678.823714.2366
23.6031-0.6496-0.12764.91261.55075.32310.05280.3123-0.16430.00860.0321-0.11330.14610.1181-0.11610.19060.00150.00930.2758-0.01880.26961.5649-5.10223.3605
37.1911.4674-2.43915.10750.39211.0088-0.5369-1.4382-1.47061.7315-0.0645-1.32120.92360.67350.47470.75660.0686-0.02990.63240.20980.66452.6001-4.314520.9086
41.8777-0.08570.58466.07563.87576.5647-0.0893-0.0635-0.00690.4494-0.34190.77080.3748-0.31840.34030.21260.0050.05160.2976-0.00010.3287-5.17890.507610.8802
54.5962-3.141-1.85985.84644.26287.33810.4293-0.28940.12021.39870.7993-0.85381.11610.5165-0.37120.55390.1058-0.29290.6303-0.13330.6729.42098.092326.7469
62.625-1.4152-0.74434.59691.34543.1039-0.0144-0.2692-0.033-0.02560.17-0.5644-0.08860.2392-0.20320.18440.0108-0.0150.2968-0.00220.27354.7366-4.34299.1224
72.3049-0.0547-1.52563.6183.09646.8081-0.0613-0.35580.04080.06930.393-0.7574-0.35960.6969-0.34340.4023-0.09050.06770.4173-0.02620.47056.67578.22519.6573
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 34 )
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 54 )
3X-RAY DIFFRACTION3chain 'A' and (resid 55 through 62 )
4X-RAY DIFFRACTION4chain 'A' and (resid 63 through 84 )
5X-RAY DIFFRACTION5chain 'A' and (resid 85 through 91 )
6X-RAY DIFFRACTION6chain 'A' and (resid 92 through 118 )
7X-RAY DIFFRACTION7chain 'A' and (resid 119 through 136 )

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