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- PDB-4rhp: Crystal structure of human COQ9 in complex with a phospholipid, N... -

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Basic information

Entry
Database: PDB / ID: 4rhp
TitleCrystal structure of human COQ9 in complex with a phospholipid, Northeast Structural Genomics Consortium Target HR5043
ComponentsUbiquinone biosynthesis protein COQ9, mitochondrial
KeywordsBIOSYNTHETIC PROTEIN / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG / all alpha-helical protein / Ubiquinone biosynthesis / mitochondrial / Mitochondrial Protein Partnership / MPP
Function / homology
Function and homology information


Ubiquinol biosynthesis / ubiquinone biosynthesis complex / isoprenoid binding / ubiquinone biosynthetic process / mitochondrial electron transport, NADH to ubiquinone / mitochondrial inner membrane / lipid binding / protein homodimerization activity / mitochondrion
Similarity search - Function
Ubiquinone biosynthesis protein COQ9 / : / Ubiquinone biosynthesis protein COQ9, N-terminal domain / COQ9 / COQ9
Similarity search - Domain/homology
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Ubiquinone biosynthesis protein COQ9, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.393 Å
AuthorsForouhar, F. / Lew, S. / Seetharaman, J. / Wang, H. / Lee, D. / Kogan, S. / Maglaqui, M. / Xiao, R. / Everett, J.K. / Montelione, G.T. ...Forouhar, F. / Lew, S. / Seetharaman, J. / Wang, H. / Lee, D. / Kogan, S. / Maglaqui, M. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) / Mitochondrial Protein Partnership (MPP)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Mitochondrial COQ9 is a lipid-binding protein that associates with COQ7 to enable coenzyme Q biosynthesis.
Authors: Lohman, D.C. / Forouhar, F. / Beebe, E.T. / Stefely, M.S. / Minogue, C.E. / Ulbrich, A. / Stefely, J.A. / Sukumar, S. / Luna-Sanchez, M. / Jochem, A. / Lew, S. / Seetharaman, J. / Xiao, R. / ...Authors: Lohman, D.C. / Forouhar, F. / Beebe, E.T. / Stefely, M.S. / Minogue, C.E. / Ulbrich, A. / Stefely, J.A. / Sukumar, S. / Luna-Sanchez, M. / Jochem, A. / Lew, S. / Seetharaman, J. / Xiao, R. / Wang, H. / Westphall, M.S. / Wrobel, R.L. / Everett, J.K. / Mitchell, J.C. / Lopez, L.C. / Coon, J.J. / Tong, L. / Pagliarini, D.J.
History
DepositionOct 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Nov 19, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Aug 14, 2019Group: Data collection / Category: computing
Revision 1.6Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquinone biosynthesis protein COQ9, mitochondrial
B: Ubiquinone biosynthesis protein COQ9, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8753
Polymers54,1832
Non-polymers6921
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-49 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.340, 97.628, 64.109
Angle α, β, γ (deg.)90.00, 95.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ubiquinone biosynthesis protein COQ9, mitochondrial


Mass: 27091.748 Da / Num. of mol.: 2 / Fragment: residues 84-318 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75208
#2: Chemical ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL


Mass: 691.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 291 K / Method: mircobatch under oil / pH: 8.5
Details: 100 mM TRIS (pH 8.5), 20% (v/v) PEG 3350, and 200 mM MgCl2 , mircobatch under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 7, 2013 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.4→48.79 Å / Num. obs: 35868 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.061 / Net I/σ(I): 15.68
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2.55 / Num. unique all: 3589 / Rsym value: 0.464 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7_650)refinement
SnBphasing
RESOLVEmodel building
XTALVIEWrefinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.393→48.79 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 1885 10.22 %RANDOM
Rwork0.1791 ---
all0.1866 35868 --
obs0.1859 18450 99.38 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.647 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 41.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.8369 Å2-0 Å2-2.2861 Å2
2---1.4375 Å2-0 Å2
3----0.3994 Å2
Refinement stepCycle: LAST / Resolution: 2.393→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3159 0 32 90 3281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083255
X-RAY DIFFRACTIONf_angle_d1.1174404
X-RAY DIFFRACTIONf_dihedral_angle_d15.3251203
X-RAY DIFFRACTIONf_chiral_restr0.074490
X-RAY DIFFRACTIONf_plane_restr0.004567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.393-2.45770.33581200.22371181X-RAY DIFFRACTION93
2.4577-2.530.27421460.20751284X-RAY DIFFRACTION100
2.53-2.61170.28611410.18471265X-RAY DIFFRACTION100
2.6117-2.7050.29031580.19591284X-RAY DIFFRACTION100
2.705-2.81330.2661380.19351273X-RAY DIFFRACTION100
2.8133-2.94140.33931540.19691274X-RAY DIFFRACTION100
2.9414-3.09640.28661570.18881258X-RAY DIFFRACTION100
3.0964-3.29040.23821470.17561274X-RAY DIFFRACTION100
3.2904-3.54430.27081400.17851309X-RAY DIFFRACTION100
3.5443-3.90090.21081540.16581280X-RAY DIFFRACTION100
3.9009-4.4650.19871280.14981289X-RAY DIFFRACTION100
4.465-5.62410.23161480.17381289X-RAY DIFFRACTION100
5.6241-48.82410.2221540.18721305X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -13.6155 Å / Origin y: -24.8997 Å / Origin z: -33.7711 Å
111213212223313233
T0.0967 Å2-0.0129 Å2-0.0085 Å2-0.1214 Å20.0034 Å2--0.1357 Å2
L0.3435 °2-0.0483 °2-0.0397 °2-0.5055 °2-0.1259 °2--0.7825 °2
S0.0059 Å °-0.048 Å °0.035 Å °0.0249 Å °-0.0578 Å °0.0049 Å °-0.0843 Å °-0.005 Å °-0 Å °
Refinement TLS groupSelection details: all

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