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- PDB-5i35: Structure of the Human mitochondrial kinase COQ8A R611K with AMPP... -

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Basic information

Entry
Database: PDB / ID: 5i35
TitleStructure of the Human mitochondrial kinase COQ8A R611K with AMPPNP (Cerebellar Ataxia and Ubiquinone Deficiency Through Loss of Unorthodox Kinase Activity)
ComponentsAtypical kinase ADCK3, mitochondrial
KeywordsTRANSFERASE / mitochondrial protein / kinase / ubiquinone biosynthesis / ubib clade kinase / Structural Genomics / PSI-2 / Protein Structure Initiative / Mitochondrial Protein Partnership / MPP / ADCK3 / Coenzyme Q biosynthesis / ADCK3_HUMAN
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Atypical kinase COQ8A, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsBingman, C.A. / Stefely, J.A. / Pagliarini, D.J. / Mitochondrial Protein Partnership (MPP)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01GM094622 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM112057-02 United States
CitationJournal: Mol.Cell / Year: 2016
Title: Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity.
Authors: Stefely, J.A. / Licitra, F. / Laredj, L. / Reidenbach, A.G. / Kemmerer, Z.A. / Grangeray, A. / Jaeg-Ehret, T. / Minogue, C.E. / Ulbrich, A. / Hutchins, P.D. / Wilkerson, E.M. / Ruan, Z. / ...Authors: Stefely, J.A. / Licitra, F. / Laredj, L. / Reidenbach, A.G. / Kemmerer, Z.A. / Grangeray, A. / Jaeg-Ehret, T. / Minogue, C.E. / Ulbrich, A. / Hutchins, P.D. / Wilkerson, E.M. / Ruan, Z. / Aydin, D. / Hebert, A.S. / Guo, X. / Freiberger, E.C. / Reutenauer, L. / Jochem, A. / Chergova, M. / Johnson, I.E. / Lohman, D.C. / Rush, M.J. / Kwiecien, N.W. / Singh, P.K. / Schlagowski, A.I. / Floyd, B.J. / Forsman, U. / Sindelar, P.J. / Westphall, M.S. / Pierrel, F. / Zoll, J. / Dal Peraro, M. / Kannan, N. / Bingman, C.A. / Coon, J.J. / Isope, P. / Puccio, H. / Pagliarini, D.J.
History
DepositionFeb 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Aug 31, 2016Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Atypical kinase ADCK3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4302
Polymers45,9231
Non-polymers5061
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-3 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.050, 59.120, 51.000
Angle α, β, γ (deg.)90.00, 97.69, 90.00
Int Tables number5
Space group name H-MC121
DetailsMonomer confirmed by gel filtration

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Components

#1: Protein Atypical kinase ADCK3, mitochondrial / Chaperone activity of bc1 complex-like / Chaperone-ABC1-like / aarF domain-containing protein kinase 3


Mass: 45923.363 Da / Num. of mol.: 1 / Mutation: R611K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADCK3, CABC1, PP265 / Plasmid: PVP68K / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: Q8NI60, Transferases; Transferring phosphorus-containing groups
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: One part of ADCK3 R611K, 0.2 mM, AMPPNP 2 mM, MgCl2, 4mM, mixed with an equal volume of sodium polyacrylate 5100, 26%; magnesium chloride, 20 mM; HEPES, 100 mM, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.96862 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 19840 / % possible obs: 100 % / Redundancy: 7.37 % / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Net I/σ(I): 12.5
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 7.61 % / Rmerge(I) obs: 1.232 / Mean I/σ(I) obs: 1.65 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→44.67 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.922 / SU B: 18.075 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25887 1556 7.8 %RANDOM
Rwork0.18346 ---
obs0.18952 18275 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 76.273 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20.8 Å2
2--1.27 Å20 Å2
3----2.22 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3105 0 31 26 3162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193207
X-RAY DIFFRACTIONr_bond_other_d0.0020.023058
X-RAY DIFFRACTIONr_angle_refined_deg2.1521.9914332
X-RAY DIFFRACTIONr_angle_other_deg1.15537034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2085383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66923.648159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.30915526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8461526
X-RAY DIFFRACTIONr_chiral_restr0.1190.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213586
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02761
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6016.5861535
X-RAY DIFFRACTIONr_mcbond_other4.5986.5851534
X-RAY DIFFRACTIONr_mcangle_it6.6289.8611917
X-RAY DIFFRACTIONr_mcangle_other6.6289.8631918
X-RAY DIFFRACTIONr_scbond_it5.3457.1041672
X-RAY DIFFRACTIONr_scbond_other5.3447.1041673
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.7710.4512416
X-RAY DIFFRACTIONr_long_range_B_refined10.05952.3353474
X-RAY DIFFRACTIONr_long_range_B_other10.05852.3293473
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 111 -
Rwork0.308 1324 -
obs--99.79 %
Refinement TLS params.Method: refined / Origin x: 50.9469 Å / Origin y: 36.1305 Å / Origin z: 18.7924 Å
111213212223313233
T0.0535 Å2-0.0046 Å20.0347 Å2-0.0274 Å2-0.0064 Å2--0.0651 Å2
L0.7755 °2-0.2354 °20.1214 °2-0.3956 °20.2083 °2--0.2599 °2
S0.0787 Å °0.0177 Å °-0.1058 Å °-0.0306 Å °0.0022 Å °0.0192 Å °-0.0408 Å °0.021 Å °-0.0809 Å °

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