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- PDB-9tvn: Structure of the Tetrapod Ancestor COQ8A in complex with AMP-PNP ... -

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Basic information

Entry
Database: PDB / ID: 9tvn
TitleStructure of the Tetrapod Ancestor COQ8A in complex with AMP-PNP and 2Mn(II)
ComponentsAtypical kinase COQ8A, mitochondrial - reconstructed tetrapod ancestor
KeywordsLIPID TRANSPORT / ATPase / CoenzymeQ biosynthesis / atypical kinase / LIPID BINDING PROTEIN
Function / homologyPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / :
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 COQ8A, mitochondrial - reconstructed tetrapod ancestor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6666
Polymers55,9261
Non-polymers7405
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-8 kcal/mol
Surface area17640 Å2
Unit cell
Length a, b, c (Å)56.456, 80.258, 87.504
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 Atypical kinase COQ8A, mitochondrial - reconstructed tetrapod ancestor


Mass: 55926.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10 mg/ml protein and 0.12 M monosaccharides mix (0.2 M D-glucose, 0.2 M D-mannose, 0.2 M D-galactose, 0.2 M L-fucose, 0.2 M D-xylose, 0.2 M N-acetyl-D-glucosamine), 0.1 M buffer system 1 pH ...Details: 10 mg/ml protein and 0.12 M monosaccharides mix (0.2 M D-glucose, 0.2 M D-mannose, 0.2 M D-galactose, 0.2 M L-fucose, 0.2 M D-xylose, 0.2 M N-acetyl-D-glucosamine), 0.1 M buffer system 1 pH 6.5 (0.5 M imidazole, 0.5 M MES monohydrate acid), 50% (v/v) precipitant mix 2 (40% (v/v) ethylene glycol, 20% (w/v) PEG 8000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS4 XE 4M / Detector: PIXEL / Date: Mar 29, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.1→46.22 Å / Num. obs: 154277 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.065 / Rrim(I) all: 0.166 / Χ2: 1.01 / Net I/σ(I): 10.6
Reflection shellResolution: 2.1→2.16 Å / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 1.166 / Num. measured all: 12229 / Num. unique obs: 1920 / CC1/2: 0.541 / Rpim(I) all: 0.501 / Rrim(I) all: 1.271 / Χ2: 1.02 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.219 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.91 / SU B: 6.583 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.21
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2552 1121 4.701 %RANDOM
Rwork0.1858 22726 --
all0.189 ---
obs-23900 99.958 %-
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: 29.387 Å2
Baniso -1Baniso -2Baniso -3
1--0.643 Å20 Å2-0 Å2
2--0.787 Å20 Å2
3----0.143 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3151 0 41 198 3390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123257
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163116
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.8544392
X-RAY DIFFRACTIONr_angle_other_deg0.5791.7717188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2335390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.507522
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.01951
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99110595
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.41310157
X-RAY DIFFRACTIONr_chiral_restr0.0820.2478
X-RAY DIFFRACTIONr_chiral_restr_other0.2710.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023776
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02751
X-RAY DIFFRACTIONr_nbd_refined0.2330.2728
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.22914
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21611
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21727
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2173
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0410.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1950.215
X-RAY DIFFRACTIONr_nbd_other0.2250.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1840.28
X-RAY DIFFRACTIONr_mcbond_it2.3842.8051563
X-RAY DIFFRACTIONr_mcbond_other2.3792.8051563
X-RAY DIFFRACTIONr_mcangle_it3.3685.0311952
X-RAY DIFFRACTIONr_mcangle_other3.3675.0331953
X-RAY DIFFRACTIONr_scbond_it3.7993.2861694
X-RAY DIFFRACTIONr_scbond_other3.7993.2861694
X-RAY DIFFRACTIONr_scangle_it5.8335.8292440
X-RAY DIFFRACTIONr_scangle_other5.8325.8282441
X-RAY DIFFRACTIONr_lrange_it7.03629.2513767
X-RAY DIFFRACTIONr_lrange_other7.02229.1233732
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
2.1-2.1540.348770.28116510.28417290.9090.94299.94220.261
2.154-2.2130.296690.25216070.25416760.9380.9551000.227
2.213-2.2770.334730.23515850.2416580.9280.9591000.207
2.277-2.3470.273900.21315100.21716000.940.9671000.185
2.347-2.4240.298830.2114660.21515490.9280.9691000.178
2.424-2.5090.274810.19414120.19814940.9540.97699.93310.161
2.509-2.6030.249760.17813780.18214550.9620.9899.93130.148
2.603-2.7090.216650.17913250.18113910.9740.9899.92810.148
2.709-2.8290.268660.17613050.1813710.950.981000.148
2.829-2.9670.245670.17712140.1812810.9560.981000.15
2.967-3.1270.286510.18911710.19312220.9530.9771000.165
3.127-3.3150.311450.20311090.20711550.9460.97599.91340.182
3.315-3.5430.298590.19510550.20111140.9520.9791000.179
3.543-3.8250.204530.1729780.17410310.970.9841000.158
3.825-4.1870.204430.1539020.1569460.9750.98799.89430.142
4.187-4.6770.222270.1498520.1518790.9720.9871000.14
4.677-5.3910.198370.1697260.177640.9820.98699.86910.157
5.391-6.580.265300.1936470.1966770.9680.9851000.174
6.58-9.2130.183230.1555070.1565300.9770.9881000.148
9.213-46.2190.35360.1563260.1593330.9690.98699.69970.147

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