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- PDB-5ekz: Crystal structure of mouse Taco1 -

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Basic information

Entry
Database: PDB / ID: 5ekz
TitleCrystal structure of mouse Taco1
ComponentsTranslational activator of cytochrome c oxidase 1
KeywordsOXIDOREDUCTASE / Mitochondria / RNA binding
Function / homology
Function and homology information


regulation of cytochrome-c oxidase activity / motor learning / TP53 Regulates Metabolic Genes / regulation of mitochondrial translation / Respiratory electron transport / mitochondrial cytochrome c oxidase assembly / mitochondrial ribosome binding / rRNA binding / mRNA binding / mitochondrion
Similarity search - Function
Transcriptional regulator TACO1-like / Transcriptional regulator TACO1-like, domain 3 / TACO1/YebC second and third domain / YebC-like / Integrase-like, N-terminal
Similarity search - Domain/homology
Translational activator of cytochrome c oxidase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsSpahr, H. / Richman, T.R. / Larsson, N.G. / Rackham, O. / Filipovska, A.
CitationJournal: Nat Commun / Year: 2016
Title: Loss of the RNA-binding protein TACO1 causes late-onset mitochondrial dysfunction in mice.
Authors: Richman, T.R. / Spahr, H. / Ermer, J.A. / Davies, S.M. / Viola, H.M. / Bates, K.A. / Papadimitriou, J. / Hool, L.C. / Rodger, J. / Larsson, N.G. / Rackham, O. / Filipovska, A.
History
DepositionNov 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Translational activator of cytochrome c oxidase 1


Theoretical massNumber of molelcules
Total (without water)32,3641
Polymers32,3641
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.550, 55.380, 92.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Translational activator of cytochrome c oxidase 1 / Coiled-coil domain-containing protein 44 / Translational activator of mitochondrially-encoded ...Coiled-coil domain-containing protein 44 / Translational activator of mitochondrially-encoded cytochrome c oxidase 1


Mass: 32364.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Taco1, Ccdc44 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8K0Z7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 1.91 Å3/Da / Density % sol: 35.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 200 mM Ammonium Nitrate, 160 mM Sodium Thiocyanate, 10 % Peg 400, and 20 % Peg 3350

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 17352 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.061 / Χ2: 1.007 / Net I/σ(I): 17.41 / Num. measured all: 108871
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2-2.070.6791.1061.7310630166116571.20399.8
2.07-2.150.8260.7092.6710251164616450.77399.9
2.15-2.250.9060.523.7310769174317410.56899.9
2.25-2.370.9540.3675.3710825175217490.499.8
2.37-2.520.9780.2338.3911561172917290.252100
2.52-2.710.9910.14712.3511135169016900.16100
2.71-2.990.9950.08918.9811255176617660.097100
2.99-3.420.9980.05328.4310474173917380.05899.9
3.42-4.310.9990.03641.4511205177817760.03999.9
4.310.9990.02946.7810766186518610.03299.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
BUSTERrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
AutoSolphasing
RefinementResolution: 2→19.468 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2209 1068 6.16 %
Rwork0.2019 16256 -
obs0.2032 17324 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.99 Å2 / Biso mean: 62.9451 Å2 / Biso min: 26.52 Å2
Refinement stepCycle: final / Resolution: 2→19.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1713 0 0 56 1769
Biso mean---48.88 -
Num. residues----221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131737
X-RAY DIFFRACTIONf_angle_d1.0622334
X-RAY DIFFRACTIONf_chiral_restr0.065262
X-RAY DIFFRACTIONf_plane_restr0.007306
X-RAY DIFFRACTIONf_dihedral_angle_d10.9991084
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0001-2.09110.33781480.294619662114
2.0911-2.20120.30021240.262120202144
2.2012-2.33890.28771230.291919812104
2.3389-2.51910.28371240.218420272151
2.5191-2.7720.23931280.220320212149
2.772-3.17160.23511380.203220352173
3.1716-3.99020.21681310.195620592190
3.9902-19.46850.1851520.172721472299
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)
14.2368-2.29311.35357.32281.17277.96060.21190.53490.141-0.26-0.0582-0.0772-0.2026-0.31380.10550.2980.0326-0.02680.40040.01090.248224.825722.956415.1874
23.3655-0.23791.05174.77861.59857.0896-0.05220.00540.3075-0.26160.3469-0.5763-0.52990.42640.06770.3312-0.03420.0040.3792-0.02960.319428.304622.84920.3523
33.1579-0.46321.26314.1171-1.20464.6940.2429-0.09-0.4197-0.36530.20480.4960.2317-0.5576-0.41750.3237-0.0428-0.06470.49490.11740.413314.27234.35710.1826
42.1169-1.85172.19412.0899-2.82353.98870.46141.2748-0.5896-2.04440.01640.80661.51250.4393-0.4290.8560.0597-0.01120.73210.09310.550310.74284.1697-0.0913
54.0074-2.27861.41518.7101-2.19543.1057-0.3682-0.58140.54270.48550.2225-0.112-0.9819-0.21170.19610.62550.0877-0.10530.662-0.04640.49195.964434.66410.1794
64.2962-0.22330.82422.73450.05525.9856-0.2323-0.51680.22060.59560.12720.1299-0.6286-0.29060.08640.48990.081-0.01850.5287-0.00530.48450.445132.9763-3.495
74.9572-3.5166-0.96362.64761.19191.8642-1.0489-1.5133-0.41142.01990.37820.4357-0.8662-1.14470.10831.45030.36920.01641.155-0.08230.7987-1.275535.523810.6753
84.9505-1.86282.48256.0902-1.55173.527-0.234-0.26610.41970.0882-0.0064-0.7667-0.63640.99330.18620.431-0.0845-0.08470.6640.0460.491311.52231.895-4.0972
93.3541-1.59422.28042.0128-0.09493.6788-0.2052-1.1596-0.29270.21190.2780.1801-0.3121-0.6947-0.23660.33730.0261-0.08320.75750.12220.32323.757321.58034.2184
104.7817-1.11480.40822.6821-0.03953.69540.105-0.79350.47090.48820.33630.737-0.273-0.974-0.2870.35640.02630.06770.62840.18450.54348.450210.169314.8634
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 74:106)A74 - 106
2X-RAY DIFFRACTION2(chain A and resid 107:129)A107 - 129
3X-RAY DIFFRACTION3(chain A and resid 130:171)A130 - 171
4X-RAY DIFFRACTION4(chain A and resid 172:179)A172 - 179
5X-RAY DIFFRACTION5(chain A and resid 180:196)A180 - 196
6X-RAY DIFFRACTION6(chain A and resid 197:221)A197 - 221
7X-RAY DIFFRACTION7(chain A and resid 222:226)A222 - 226
8X-RAY DIFFRACTION8(chain A and resid 227:244)A227 - 244
9X-RAY DIFFRACTION9(chain A and resid 245:270)A245 - 270
10X-RAY DIFFRACTION10(chain A and resid 271:294)A271 - 294

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