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Basic information

Entry
Database: PDB / ID: 8p6g
TitleCrystal structure of the improved version of the Genetically Encoded Green Calcium Indicator YTnC2-5
ComponentsGenetically Encoded Green Calcium Indicator YTnC2-5 based on Troponin C from toadfish
KeywordsFLUORESCENT PROTEIN / calcium sensor / indicator / TNC / troponin / GECI / YTnC2
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBoyko, K.M. / Nikolaeva, A.Y. / Subach, O.M. / Vlaskina, A.V. / Agapova, Y.K. / Popov, V.O. / Subach, F.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation075-15-2021-1354 Russian Federation
CitationJournal: Febs Open Bio / Year: 2023
Title: YTnC2, an improved genetically encoded green calcium indicator based on toadfish troponin C.
Authors: Subach, O.M. / Vlaskina, A.V. / Agapova, Y.K. / Nikolaeva, A.Y. / Varizhuk, A.M. / Podgorny, O.V. / Piatkevich, K.D. / Patrushev, M.V. / Boyko, K.M. / Subach, F.V.
History
DepositionMay 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Genetically Encoded Green Calcium Indicator YTnC2-5 based on Troponin C from toadfish
D: Genetically Encoded Green Calcium Indicator YTnC2-5 based on Troponin C from toadfish
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8584
Polymers71,6462
Non-polymers2122
Water3,855214
1
B: Genetically Encoded Green Calcium Indicator YTnC2-5 based on Troponin C from toadfish
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9292
Polymers35,8231
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Genetically Encoded Green Calcium Indicator YTnC2-5 based on Troponin C from toadfish
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9292
Polymers35,8231
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.736, 65.736, 315.036
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Genetically Encoded Green Calcium Indicator YTnC2-5 based on Troponin C from toadfish


Mass: 35822.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55.18 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.2M Sodium fluoride, 0.1M Bis-tris propane, 20% PEG 3350 pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→46.14 Å / Num. obs: 55880 / % possible obs: 100 % / Redundancy: 20.2 % / CC1/2: 0.992 / Rmerge(I) obs: 0.313 / Rpim(I) all: 0.071 / Rrim(I) all: 0.321 / Χ2: 1.02 / Net I/σ(I): 6.5 / Num. measured all: 1130475
Reflection shellResolution: 1.95→2 Å / % possible obs: 100 % / Redundancy: 19.1 % / Rmerge(I) obs: 3.567 / Num. measured all: 76035 / Num. unique obs: 3979 / CC1/2: 0.468 / Rpim(I) all: 0.83 / Rrim(I) all: 3.663 / Χ2: 1.04 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→46.14 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.107 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22883 2837 5.1 %RANDOM
Rwork0.18335 ---
obs0.1857 52835 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.401 Å2
Baniso -1Baniso -2Baniso -3
1-5.73 Å20 Å20 Å2
2--5.73 Å20 Å2
3----11.46 Å2
Refinement stepCycle: 1 / Resolution: 1.95→46.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3880 0 14 214 4108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0124016
X-RAY DIFFRACTIONr_bond_other_d0.0030.0163683
X-RAY DIFFRACTIONr_angle_refined_deg2.0291.6595427
X-RAY DIFFRACTIONr_angle_other_deg0.7791.5828482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1755484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.835530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.35610654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1090.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024723
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02938
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6983.0111948
X-RAY DIFFRACTIONr_mcbond_other3.693.011947
X-RAY DIFFRACTIONr_mcangle_it4.8095.422425
X-RAY DIFFRACTIONr_mcangle_other4.8095.422426
X-RAY DIFFRACTIONr_scbond_it3.8263.1852068
X-RAY DIFFRACTIONr_scbond_other3.8253.1852069
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1675.7683002
X-RAY DIFFRACTIONr_long_range_B_refined6.86730.084149
X-RAY DIFFRACTIONr_long_range_B_other6.85929.664119
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 175 -
Rwork0.219 3946 -
obs--99.37 %
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)
10.4679-0.04450.07650.22230.07740.2547-0.01880.03220.03210.04450.01140.00260.0532-0.01250.00740.0408-0.00250.00010.00580.00260.002333.725-21.802-0.5933
20.17990.0626-0.11130.4688-0.01170.190.03850.0113-0.01820.0026-0.043-0.0212-0.0217-0.03650.00440.01250.0124-0.00360.03420.00210.002730.9561-16.9351-37.8732
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B5 - 401
2X-RAY DIFFRACTION2D6 - 401

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