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- PDB-7udp: Crystal structure of COQ8A-CA157 inhibitor complex in space group C2 -

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Basic information

Entry
Database: PDB / ID: 7udp
TitleCrystal structure of COQ8A-CA157 inhibitor complex in space group C2
ComponentsAtypical kinase COQ8A, mitochondrial
KeywordsTRANSFERASE / CoQ biosynthesis / kinase-like
Function / homology
Function and homology information


Ubiquinol biosynthesis / extrinsic component of mitochondrial inner membrane / Transferases; Transferring phosphorus-containing groups / ubiquinone biosynthetic process / phosphorylation / enzyme activator activity / ADP binding / kinase activity / protein kinase activity / mitochondrion / ATP binding
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 / molecular replacement / Resolution: 2.01 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

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Assembly

Deposited unit
A: Atypical kinase COQ8A, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5832
Polymers45,2481
Non-polymers3351
Water32418
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.210, 56.379, 48.684
Angle α, β, γ (deg.)90.000, 98.390, 90.000
Int Tables number5
Space group name H-MC121

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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.: 1
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.: 1 / Source method: obtained synthetically / Formula: C19H17N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Crystals were grown in a MRC SD2 plate set by a STP Labtech Mosquito. Protein at 17.89 mg/ml (390 uM) and 500 uM CA157 were inc for 30 min at ambient temp prior to setting the plate. The ...Details: Crystals were grown in a MRC SD2 plate set by a STP Labtech Mosquito. Protein at 17.89 mg/ml (390 uM) and 500 uM CA157 were inc for 30 min at ambient temp prior to setting the plate. The droplet providing the crystal used for data collection and refinement was 200 nL of protein-CA157 solution and 25 nL reservoir, 0.65 M sodium succinate pH 7, 0.1M HEPPS buffer, pH 8.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03323 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03323 Å / Relative weight: 1
ReflectionResolution: 2.01→37.4 Å / Num. obs: 27346 / % possible obs: 99.8 % / Redundancy: 6.708 % / Biso Wilson estimate: 65.58 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.034 / Rrim(I) all: 0.037 / Χ2: 0.91 / Net I/σ(I): 20.71 / Num. measured all: 183425 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.01-2.066.8741.561.0719960.4721.687100
2.06-2.116.5891.1361.4919530.6341.23499.9
2.11-2.176.9020.7162.4419250.8030.77499.9
2.17-2.246.6860.533.2918460.8810.57599.8
2.24-2.326.9670.3644.918000.940.39399.9
2.32-2.46.9280.2417.2617240.9760.26100
2.4-2.496.8660.16810.2216840.9870.18199.9
2.49-2.596.640.1213.516240.9930.13100
2.59-2.76.8460.09417.6615690.9960.10299.8
2.7-2.846.7360.07123.0714680.9970.077100
2.84-2.996.9020.05530.7314110.9980.05999.7
2.99-3.176.7470.04436.4113260.9990.048100
3.17-3.396.490.03841.2812740.9990.04199.8
3.39-3.666.4110.03445.5511630.9990.03799.7
3.66-4.016.7010.03149.310990.9990.03399.6
4.01-4.486.4920.0350.859710.9990.03299.6
4.48-5.186.3420.0350.788650.9990.03399.8
5.18-6.346.2410.03250.457440.9990.03499.5
6.34-8.976.2030.02951.035720.9990.03299.1
8.97-37.460.02551.043320.9990.02898.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XSCALEFeb 5, 2021data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
XDSMar 15, 2019data reduction
autoPROC1.0.5 20190923data processing
JBluIce-EPICS2019-03data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5i35

5i35


Resolution: 2.01→37.4 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2794 2129 7.79 %
Rwork0.2397 25209 -
obs0.2427 27338 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 266.9 Å2 / Biso mean: 97.6354 Å2 / Biso min: 47.11 Å2
Refinement stepCycle: final / Resolution: 2.01→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3053 0 42 18 3113
Biso mean--71 65.19 -
Num. residues----378
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.01-2.050.36851400.373916541794100
2.05-2.10.41291420.382716711813100
2.1-2.160.41211410.383416601801100
2.16-2.220.3681420.358916811823100
2.22-2.30.38751410.345816671808100
2.3-2.380.3381420.318916741816100
2.38-2.470.32281400.322516651805100
2.47-2.580.37671440.320816961840100
2.58-2.720.40191400.355616571797100
2.72-2.890.36531440.32516941838100
2.89-3.110.33191420.29116821824100
3.11-3.430.30621410.268516751816100
3.43-3.920.24931410.226116911832100
3.92-4.940.24471420.194917031845100
4.94-37.40.23641470.19741739188699
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)
12.5695-2.13810.22463.62360.31012.52290.1763-0.0478-0.0670.05730.03240.28840.032-0.0876-0.21880.3594-0.06190.01240.4623-0.07270.453648.824636.659813.3557
24.2926-2.3813-0.75365.3747-1.31423.26350.2419-0.3410.63080.55310.0904-0.0136-0.7038-0.152-0.3260.5915-0.00730.06570.63-0.12290.601748.404947.5110.4824
33.8188-1.4880.77263.23922.33652.41480.2793-0.4257-0.15460.1620.01360.1410.3958-0.3349-0.36590.7485-0.06310.00830.54130.0930.550658.71426.829130.0542
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 383 through 562 )A383 - 562
2X-RAY DIFFRACTION2chain 'A' and (resid 563 through 644 )A563 - 644
3X-RAY DIFFRACTION3chain 'A' and (resid 258 through 382 )A258 - 382

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