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- PDB-7udq: Crystal structure of COQ8A-CA157 inhibitor complex in space group P1 -

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Basic information

Entry
Database: PDB / ID: 7udq
TitleCrystal structure of COQ8A-CA157 inhibitor complex in space group P1
ComponentsAtypical kinase COQ8A, mitochondrial
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / CoQ biosynthesis / kinase-like / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Ubiquinol biosynthesis / ubiquinone biosynthetic process / Transferases; Transferring phosphorus-containing groups / phosphorylation / ADP binding / kinase activity / mitochondrion / ATP binding / membrane
Similarity search - Function
ABC1 atypical kinase-like domain / ADCK3-like domain / : / ABC1 atypical kinase-like domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-MVS / Atypical kinase COQ8A, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBingman, C.A. / Murray, N. / Smith, R.W. / Pagliarini, D.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM131795 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008505 United States
National Science Foundation (NSF, United States)DGE-1747503 United States
CitationJournal: Nat.Chem.Biol. / Year: 2023
Title: Small-molecule inhibition of the archetypal UbiB protein COQ8.
Authors: Murray, N.H. / Asquith, C.R.M. / Fang, Z. / East, M.P. / Ptak, N. / Smith, R.W. / Vasta, J.D. / Zimprich, C.A. / Corona, C.R. / Robers, M.B. / Johnson, G.L. / Bingman, C.A. / Pagliarini, D.J.
History
DepositionMar 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Atypical kinase COQ8A, mitochondrial
B: Atypical kinase COQ8A, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2136
Polymers90,4962
Non-polymers7174
Water4,792266
1
A: Atypical kinase COQ8A, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6294
Polymers45,2481
Non-polymers3813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Atypical kinase COQ8A, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5832
Polymers45,2481
Non-polymers3351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.273, 54.859, 80.012
Angle α, β, γ (deg.)109.790, 94.620, 92.110
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Atypical kinase COQ8A, mitochondrial / Chaperone activity of bc1 complex-like / Chaperone-ABC1-like / Coenzyme Q protein 8A / aarF domain- ...Chaperone activity of bc1 complex-like / Chaperone-ABC1-like / Coenzyme Q protein 8A / aarF domain-containing protein kinase 3


Mass: 45247.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COQ8A, ADCK3, CABC1, PP265 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8NI60, Transferases; Transferring phosphorus-containing groups
#2: Chemical ChemComp-MVS / 4-[(3,4,5-trimethoxyphenyl)amino]quinoline-7-carbonitrile


Mass: 335.357 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H17N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Crystals were grown in a MRC SD2 plate set by a STP Labtech Mosquito. Protein at 17.89 mg/ml (390 uM) was incubated with 500 uM CA157 for 30 min at ambient temperature prior to setup. The ...Details: Crystals were grown in a MRC SD2 plate set by a STP Labtech Mosquito. Protein at 17.89 mg/ml (390 uM) was incubated with 500 uM CA157 for 30 min at ambient temperature prior to setup. The drop producing this data set was 200 nL protein-CA157 solution was mixed with 300 nL of 0.6 M sodium succinate, pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033149 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033149 Å / Relative weight: 1
ReflectionResolution: 1.9→38.72 Å / Num. obs: 58799 / % possible obs: 97 % / Redundancy: 3.601 % / Biso Wilson estimate: 41.87 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.074 / Χ2: 0.901 / Net I/σ(I): 9.45 / Num. measured all: 211758 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.953.7171.2361.1115985447643010.4731.44596.1
1.95-23.6770.891.6115595439642410.6321.04496.5
2-2.063.6120.6532.214720422640750.7420.76996.4
2.06-2.123.4380.4752.8513684412739800.8180.56696.4
2.12-2.193.6030.3733.7814034402838950.8920.43996.7
2.19-2.273.5620.34.5113283383137290.9190.35597.3
2.27-2.363.7890.225.9913769373936340.9610.25797.2
2.36-2.453.7640.187.1113060356534700.9720.2197.3
2.45-2.563.7040.1478.4412546348133870.980.17297.3
2.56-2.693.6710.1229.9911824330132210.9850.14397.6
2.69-2.833.5690.09811.8810917312930590.9880.11697.8
2.83-33.3520.08113.829649297128790.9890.09796.9
3-3.213.430.06516.429313280327150.9910.07796.9
3.21-3.473.5740.05619.398957257325060.9940.06697.4
3.47-3.83.6470.05121.518443236823150.9960.0697.8
3.8-4.253.5850.0522.077589217121170.9940.05997.5
4.25-4.913.5380.04722.696539188118480.9950.05598.2
4.91-6.013.3380.04821.775237162515690.9940.05796.6
6.01-8.53.5090.04622.784183122711920.9960.05597.1
8.5-38.723.650.04424.3624316856660.9960.05297.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
JBluIce-EPICS2019-3data collection
XDS20210205data reduction
autoPROC1.0.5 (20210224)data scaling
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5i35

5i35


Resolution: 1.9→38.72 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 26.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2387 2463 4.2 %
Rwork0.1916 56247 -
obs0.1935 58710 97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.33 Å2 / Biso mean: 61.8219 Å2 / Biso min: 27.92 Å2
Refinement stepCycle: final / Resolution: 1.9→38.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6036 0 86 266 6388
Biso mean--42.31 51.31 -
Num. residues----747
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.940.3251430.32323101324496
1.94-1.980.34321450.28053044318996
1.98-2.020.28891380.26913132327096
2.02-2.070.27981340.25263115324996
2.07-2.120.27921300.24093143327397
2.12-2.170.30891240.2243133325797
2.17-2.240.26771410.22353089323097
2.24-2.310.29511470.2163127327497
2.31-2.390.24611300.21163167329797
2.39-2.490.27561490.21193112326197
2.49-2.60.28491280.21273125325397
2.6-2.740.26731200.22783192331298
2.74-2.910.2581170.21963122323997
2.91-3.140.26291290.21463113324296
3.14-3.450.25341420.20393135327797
3.45-3.950.20931530.17183129328298
3.95-4.980.1911480.14593145329398
4.98-38.720.22511450.1713123326897
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)
12.8013-2.5777-0.1513.07561.26081.784-0.4743-0.6648-0.38020.9040.52510.20580.37570.2002-0.12890.5796-0.02430.08820.73650.04910.40627.972424.249963.9305
24.9529-1.9801-1.12542.24320.35543.07660.02740.098-0.1321-0.095-0.1495-0.0876-0.13560.17350.12940.2998-0.07170.01060.3235-0.00640.269925.032430.990159.1738
33.74443.25040.14136.57730.76790.6982-0.014-0.21220.07480.0839-0.04730.212-0.1198-0.08650.06370.26170.0565-0.02440.40710.00020.25885.901727.092857.1327
41.8522-0.5186-0.34783.15581.17444.5259-0.08610.096-0.0722-0.20710.0769-0.08070.19760.2170.02440.3510.02580.00480.37250.01860.30917.32959.579545.2338
53.86562.8342-2.00463.4071-2.77232.5963-0.25010.1394-0.0571-0.33860.18360.19680.1509-0.33670.02690.4093-0.02670.00680.3583-0.06320.3425-30.698555.914711.9408
60.7912-0.1299-0.03482.1515-1.22121.75-0.0701-0.0908-0.00970.0415-0.0178-0.0265-0.00470.03880.09740.3307-0.04350.00310.3785-0.03130.2779-15.313443.300324.9575
76.17630.01241.53778.6418-3.81163.37880.01840.2617-0.45410.1792-0.1526-0.1885-0.26650.22670.11030.3809-0.0372-0.04740.3612-0.07830.4312.8332.289262.6925
85.00270.5015-2.53774.37710.87932.40520.01910.20520.05990.01520.0411-0.1155-0.02530.173-0.05790.2998-0.033-0.06280.33740.00710.4555-17.916758.610511.396
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 261 through 320 )A261 - 320
2X-RAY DIFFRACTION2chain 'A' and (resid 321 through 406 )A321 - 406
3X-RAY DIFFRACTION3chain 'A' and (resid 407 through 505 )A407 - 505
4X-RAY DIFFRACTION4chain 'A' and (resid 506 through 646 )A506 - 646
5X-RAY DIFFRACTION5chain 'B' and (resid 258 through 381 )B258 - 381
6X-RAY DIFFRACTION6chain 'B' and (resid 382 through 644 )B382 - 644
7X-RAY DIFFRACTION7chain 'A' and resid 701A701
8X-RAY DIFFRACTION8chain 'B' and resid 701B701

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