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- PDB-8grf: Crystal structure of F-box protein in the ternary complex with ad... -

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Basic information

Entry
Database: PDB / ID: 8grf
TitleCrystal structure of F-box protein in the ternary complex with adaptor protein Skp1(DL) and its substrate
Components
  • Citrate synthase
  • E3 ubiquitin ligase complex SCF subunit
  • F-box protein UCC1
KeywordsTRANSFERASE/LIGASE / F-box protein / glyoxylate cycle / E3 ubiquitin ligase / TRANSFERASE / TRANSFERASE-LIGASE complex
Function / homology
Function and homology information


: / citrate metabolic process / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / cullin family protein binding / tricarboxylic acid cycle / mitotic cell cycle / carbohydrate metabolic process / protein ubiquitination / mitochondrial matrix / nucleus / cytoplasm
Similarity search - Function
Citrate synthase, eukaryotic-type / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / Citrate synthase / Citrate synthase-like, small alpha subdomain ...Citrate synthase, eukaryotic-type / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
E3 ubiquitin ligase complex SCF subunit / Citrate synthase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsNishio, K. / Nakatsukasa, K. / Kamura, T. / Mizushima, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H03198 Japan
Japan Society for the Promotion of Science (JSPS)24112009 Japan
CitationJournal: Sci Adv / Year: 2023
Title: Defective import of mitochondrial metabolic enzyme elicits ectopic metabolic stress.
Authors: Nishio, K. / Kawarasaki, T. / Sugiura, Y. / Matsumoto, S. / Konoshima, A. / Takano, Y. / Hayashi, M. / Okumura, F. / Kamura, T. / Mizushima, T. / Nakatsukasa, K.
History
DepositionSep 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Citrate synthase
B: Citrate synthase
C: F-box protein UCC1
D: E3 ubiquitin ligase complex SCF subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,75914
Polymers168,1384
Non-polymers62110
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.407, 150.976, 160.384
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Citrate synthase


Mass: 51476.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CIT2, GI527_G0000583 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5Q445
#2: Protein F-box protein UCC1


Mass: 42828.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: W303-1a / Production host: Escherichia coli (E. coli)
#3: Protein E3 ubiquitin ligase complex SCF subunit


Mass: 22357.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SKP1, GI527_G0001262 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5Q435
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.79 Å3/Da / Density % sol: 55.87 %
Description: The entry contains friedel pairs in I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 70 mM Na citrate pH 5.5, 10.5% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.53→36.64 Å / Num. obs: 63124 / % possible obs: 99.24 % / Redundancy: 6.9 % / Biso Wilson estimate: 51.24 Å2 / CC1/2: 0.997 / Net I/σ(I): 24.58
Reflection shellResolution: 2.53→2.62 Å / Mean I/σ(I) obs: 4.09 / Num. unique obs: 6158 / CC1/2: 0.828

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.53→36.64 Å / SU ML: 0.3941 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.936
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: The entry contains friedel pairs in I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2477 3783 3.15 %
Rwork0.2153 116431 -
obs0.2164 63066 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.35 Å2
Refinement stepCycle: LAST / Resolution: 2.53→36.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10914 0 40 158 11112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001711287
X-RAY DIFFRACTIONf_angle_d0.425615291
X-RAY DIFFRACTIONf_chiral_restr0.03731668
X-RAY DIFFRACTIONf_plane_restr0.00351963
X-RAY DIFFRACTIONf_dihedral_angle_d11.1744202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.560.37711220.3284023X-RAY DIFFRACTION90.15
2.56-2.590.36531370.3174313X-RAY DIFFRACTION99.51
2.59-2.630.36981630.32614291X-RAY DIFFRACTION99.78
2.63-2.670.44581290.36974344X-RAY DIFFRACTION97.94
2.67-2.710.45961640.37614157X-RAY DIFFRACTION97.72
2.71-2.750.37771170.29174417X-RAY DIFFRACTION99.93
2.75-2.790.32291540.27954304X-RAY DIFFRACTION99.96
2.79-2.840.30771420.26934355X-RAY DIFFRACTION100
2.84-2.890.31761420.26464354X-RAY DIFFRACTION100
2.89-2.950.29391330.24334406X-RAY DIFFRACTION99.96
2.95-3.010.26951360.23994345X-RAY DIFFRACTION100
3.01-3.070.31361500.24274376X-RAY DIFFRACTION100
3.07-3.150.28371450.25044340X-RAY DIFFRACTION100
3.15-3.220.21421340.24154370X-RAY DIFFRACTION99.96
3.22-3.310.31811480.23574308X-RAY DIFFRACTION99.98
3.31-3.410.27651430.24094384X-RAY DIFFRACTION99.93
3.41-3.520.32041290.25014364X-RAY DIFFRACTION99.03
3.52-3.650.23921660.22164302X-RAY DIFFRACTION99.73
3.65-3.790.28241350.23164350X-RAY DIFFRACTION99.51
3.79-3.960.23811340.22923960X-RAY DIFFRACTION91.32
3.96-4.170.21631430.17634356X-RAY DIFFRACTION99.98
4.17-4.430.18551240.16954370X-RAY DIFFRACTION100
4.43-4.780.16961510.15844352X-RAY DIFFRACTION100
4.78-5.250.20751410.17264354X-RAY DIFFRACTION99.98
5.26-6.010.23571290.19394385X-RAY DIFFRACTION99.98
6.01-7.570.19531400.19554346X-RAY DIFFRACTION100
7.57-36.640.17061320.15664205X-RAY DIFFRACTION96.21

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