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- PDB-9tvk: Structure of the Tetrapod Ancestor COQ8B in complex with ADP and ... -

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Basic information

Entry
Database: PDB / ID: 9tvk
TitleStructure of the Tetrapod Ancestor COQ8B in complex with ADP and 2Mn(II)
ComponentsAtypical kinase COQ8B, mitochondrial
KeywordsLIPID TRANSPORT / ATPase / CoenzymeQ biosynthesis / atypical kinase / LIPID BINDING PROTEIN
Function / homologyADENOSINE-5'-DIPHOSPHATE / BROMIDE ION / IODIDE ION / :
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.398 Å
AuthorsGottinger, A. / Mattevi, A.
Funding supportEuropean Union, Italy, 2items
OrganizationGrant numberCountry
European Research Council (ERC)101094471European Union
Italian Association for Cancer Research28754 Italy
CitationJournal: To Be Published
Title: COQ8 chaperones coenzyme Q lipid intermediates through ATP-driven structural gating
Authors: Gottinger, A. / Mattevi, A.
History
DepositionJan 12, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Atypical kinase COQ8B, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,34015
Polymers55,2181
Non-polymers1,12214
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-77 kcal/mol
Surface area17500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.488, 150.488, 150.488
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Atypical kinase COQ8B, mitochondrial / Atypical kinase COQ8B / mitochondrial - reconstructed tetrapod ancestor


Mass: 55218.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Synthetic sequence - reconstructed tetrapod ancestor
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 187 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#6: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15 mg/ml protein and 0.09 M halogens mix (0.3 M sodium fluoride, 0.3 M sodium bromide, 0.3 M sodium iodide), 0.1 M buffer system 2 pH 7.5 (0.5 M sodium Hepes, 0.5 M bicine), 50% (v/v) ...Details: 15 mg/ml protein and 0.09 M halogens mix (0.3 M sodium fluoride, 0.3 M sodium bromide, 0.3 M sodium iodide), 0.1 M buffer system 2 pH 7.5 (0.5 M sodium Hepes, 0.5 M bicine), 50% (v/v) precipitant mix 4 (25% (v/v) MPD, 25% (w/v) PEG 1000, 25% (w/v) PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87312815798028 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 12, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87312815798028 Å / Relative weight: 1
ReflectionResolution: 2.398→106.411 Å / Num. obs: 23456 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rsym value: 0.144 / Net I/σ(I): 8.3
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 2399 / CC1/2: 0.615 / Rsym value: 1.153

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
MOLREPphasing
Aimlessdata scaling
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.398→106.411 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.253 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / ESU R: 0.262 / ESU R Free: 0.22
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2374 1180 5.043 %
Rwork0.1844 22217 -
all0.187 --
obs-23397 99.898 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 51.862 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.398→106.411 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2968 0 40 173 3181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123071
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162929
X-RAY DIFFRACTIONr_angle_refined_deg1.9181.854144
X-RAY DIFFRACTIONr_angle_other_deg0.6561.7786732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3185366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.669529
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.00751
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.5310549
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.12810154
X-RAY DIFFRACTIONr_chiral_restr0.0910.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023641
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02750
X-RAY DIFFRACTIONr_nbd_refined0.230.2716
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.22659
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21524
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21703
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2146
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.4580.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2650.218
X-RAY DIFFRACTIONr_nbd_other0.1720.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1870.27
X-RAY DIFFRACTIONr_mcbond_it5.5355.1721470
X-RAY DIFFRACTIONr_mcbond_other5.4595.1731470
X-RAY DIFFRACTIONr_mcangle_it7.9589.2611834
X-RAY DIFFRACTIONr_mcangle_other7.9559.2661835
X-RAY DIFFRACTIONr_scbond_it6.655.631601
X-RAY DIFFRACTIONr_scbond_other6.6495.631601
X-RAY DIFFRACTIONr_scangle_it10.08110.1162310
X-RAY DIFFRACTIONr_scangle_other10.07910.1142311
X-RAY DIFFRACTIONr_lrange_it12.73649.2773606
X-RAY DIFFRACTIONr_lrange_other12.69149.1133574
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.398-2.460.338910.30315800.30516720.9180.93799.94020.293
2.46-2.5280.387850.29715710.30116590.8980.94199.81920.282
2.528-2.6010.313870.26215160.26416030.9180.9531000.244
2.601-2.6810.324820.25914610.26215450.9340.95899.87060.238
2.681-2.7690.288650.24614780.24815430.9480.9621000.224
2.769-2.8660.277580.2313820.23214410.9450.96599.93060.204
2.866-2.9740.259660.21513810.21714470.9570.971000.19
2.974-3.0950.25720.20112890.20413610.9590.9741000.176
3.095-3.2330.297750.19312480.19913230.9410.9761000.172
3.233-3.3910.232610.18812120.1912730.9660.9781000.166
3.391-3.5740.224550.16811380.17111930.9660.9831000.149
3.574-3.790.223570.15510950.15911530.9710.98799.91330.141
3.79-4.0520.229710.14910080.15410810.9680.98799.8150.133
4.052-4.3760.165420.1329710.13410130.9820.9891000.119
4.376-4.7930.158430.1179040.1199480.9850.99199.89450.103
4.793-5.3570.199410.1298130.1338560.9730.9999.76640.116
5.357-6.1830.221430.187310.1837740.9750.9811000.162
6.183-7.5660.323350.1886280.1946630.9490.9791000.171
7.566-10.6730.164360.1754980.1745350.9810.98299.81310.159
10.673-106.4110.22150.2513130.253380.9610.94797.04140.223

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