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- PDB-4ped: Mitochondrial ADCK3 employs an atypical protein kinase-like fold ... -

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Basic information

Entry
Database: PDB / ID: 4ped
TitleMitochondrial ADCK3 employs an atypical protein kinase-like fold to enable coenzyme Q biosynthes
ComponentsChaperone activity of bc1 complex-like, mitochondrial
KeywordsTRANSFERASE / Protein Kinase-like / Coenzyme Q biosynthesis / Mitochondrial / Membrane associated / Structural Genomics / PSI-Biology / Mitochondrial Protein Partnership / MPP
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups / ubiquinone biosynthetic process / ADP binding / kinase activity / phosphorylation / 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
Atypical kinase COQ8A, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.64 Å
AuthorsBingman, C.A. / Smith, R. / Joshi, S. / Stefely, J.A. / Reidenbach, A.G. / Ulbrich, A. / Oruganty, O. / Floyd, B.J. / Jochem, A. / Saunders, J.M. ...Bingman, C.A. / Smith, R. / Joshi, S. / Stefely, J.A. / Reidenbach, A.G. / Ulbrich, A. / Oruganty, O. / Floyd, B.J. / Jochem, A. / Saunders, J.M. / Johnson, I.E. / Wrobel, R.L. / Barber, G.E. / Lee, D. / Li, S. / Kannan, N. / Coon, J.J. / Pagliarini, D.J. / Mitochondrial Protein Partnership (MPP)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01GM094622 United States
CitationJournal: Mol.Cell / Year: 2015
Title: Mitochondrial ADCK3 Employs an Atypical Protein Kinase-like Fold to Enable Coenzyme Q Biosynthesis.
Authors: Stefely, J.A. / Reidenbach, A.G. / Ulbrich, A. / Oruganty, K. / Floyd, B.J. / Jochem, A. / Saunders, J.M. / Johnson, I.E. / Minogue, C.E. / Wrobel, R.L. / Barber, G.E. / Lee, D. / Li, S. / ...Authors: Stefely, J.A. / Reidenbach, A.G. / Ulbrich, A. / Oruganty, K. / Floyd, B.J. / Jochem, A. / Saunders, J.M. / Johnson, I.E. / Minogue, C.E. / Wrobel, R.L. / Barber, G.E. / Lee, D. / Li, S. / Kannan, N. / Coon, J.J. / Bingman, C.A. / Pagliarini, D.J.
History
DepositionApr 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Jan 21, 2015Group: Database references
Revision 1.3Feb 4, 2015Group: Derived calculations
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: 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: Chaperone activity of bc1 complex-like, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1443
Polymers45,9511
Non-polymers1922
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)148.671, 54.557, 45.009
Angle α, β, γ (deg.)90.00, 94.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Chaperone activity of bc1 complex-like, mitochondrial / Chaperone-ABC1-like / aarF domain-containing protein kinase 3


Mass: 45951.379 Da / Num. of mol.: 1 / Fragment: UNP residues 204-595
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADCK3, CABC1, PP265 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8NI60, Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.92 % / Description: Monoclinic rhomb-shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Seeded microbatch experiment, 5 mg/mL protein 12.5% PEG 3350, 50 mM HEPES pH 7.5, 5 mM MgCl2, 150 mM Am2SO4, 0.15 mM TCEP, 5 microliter sitting drop in bridge of VDX plate, equilibrated ...Details: Seeded microbatch experiment, 5 mg/mL protein 12.5% PEG 3350, 50 mM HEPES pH 7.5, 5 mM MgCl2, 150 mM Am2SO4, 0.15 mM TCEP, 5 microliter sitting drop in bridge of VDX plate, equilibrated against 12.5% PEG 3350, 50 mM HEPES pH 7.5, 150 mM Am2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 15, 2013
RadiationMonochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 69420 / % possible obs: 97 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 23
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.893 / Mean I/σ(I) obs: 1.5 / % possible all: 94.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXphasing
ARPmodel building
PHENIXmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: SAD / Resolution: 1.64→36.634 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.211 3478 5.01 %
Rwork0.1649 --
obs0.1672 69420 80.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.64→36.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 0 10 267 3405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123308
X-RAY DIFFRACTIONf_angle_d1.4334488
X-RAY DIFFRACTIONf_dihedral_angle_d15.8441281
X-RAY DIFFRACTIONf_chiral_restr0.06484
X-RAY DIFFRACTIONf_plane_restr0.007586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.66110.2832410.2564803X-RAY DIFFRACTION25
1.6611-1.68480.2754690.2511104X-RAY DIFFRACTION33
1.6848-1.710.2448710.24821362X-RAY DIFFRACTION42
1.71-1.73670.2513890.22921654X-RAY DIFFRACTION50
1.7367-1.76520.2073750.21511770X-RAY DIFFRACTION53
1.7652-1.79560.23491000.20161868X-RAY DIFFRACTION57
1.7956-1.82820.22641010.1932052X-RAY DIFFRACTION62
1.8282-1.86340.24241100.18742299X-RAY DIFFRACTION69
1.8634-1.90140.19091350.18842459X-RAY DIFFRACTION75
1.9014-1.94280.2361590.17752647X-RAY DIFFRACTION81
1.9428-1.9880.24721660.18082830X-RAY DIFFRACTION87
1.988-2.03770.2191940.17242987X-RAY DIFFRACTION92
2.0377-2.09280.2271870.17213182X-RAY DIFFRACTION97
2.0928-2.15430.23291780.16463177X-RAY DIFFRACTION97
2.1543-2.22390.20091330.15363236X-RAY DIFFRACTION97
2.2239-2.30330.251630.15823210X-RAY DIFFRACTION98
2.3033-2.39560.1931640.15953286X-RAY DIFFRACTION98
2.3956-2.50460.20831730.1563186X-RAY DIFFRACTION98
2.5046-2.63660.22481760.16563267X-RAY DIFFRACTION98
2.6366-2.80170.22231360.17023217X-RAY DIFFRACTION98
2.8017-3.01790.19411850.17663274X-RAY DIFFRACTION99
3.0179-3.32150.19971750.17273232X-RAY DIFFRACTION99
3.3215-3.80160.1931630.14913280X-RAY DIFFRACTION99
3.8016-4.7880.21541380.12643298X-RAY DIFFRACTION99
4.788-36.64270.18061970.16063262X-RAY DIFFRACTION100
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)
11.06910.0070.15271.9647-0.44921.4901-0.016-0.12250.02590.02240.022-0.15540.02660.0082-0.00860.06650.00890.00420.0931-0.02010.078962.300812.4428.9541
20.9602-0.36930.17750.49950.29720.76570.0891-0.2136-0.22230.08110.0482-0.05470.1385-0.0679-0.01970.1274-0.0214-0.03430.09020.03620.149557.0634-0.613727.9839
30.6050.21340.22720.9905-0.54640.74030.12370.0339-0.0876-0.0356-0.0613-0.02150.09050.0029-0.05640.07170.01070.00750.0737-0.01240.060456.11483.57949.0581
41.0643-0.7203-0.12380.6765-0.18610.56320.00970.0130.0393-0.02670.00250.026-0.0238-0.11870.00150.07030.0120.00550.0859-0.01250.060444.600521.285911.9981
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 258 through 306 )
2X-RAY DIFFRACTION2chain 'A' and (resid 307 through 407 )
3X-RAY DIFFRACTION3chain 'A' and (resid 408 through 505 )
4X-RAY DIFFRACTION4chain 'A' and (resid 506 through 644 )

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