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- PDB-8gre: F-box protein in complex with skp1(FL) and substrate -

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Basic information

Entry
Database: PDB / ID: 8gre
TitleF-box protein in complex with skp1(FL) and substrate
Components
  • Citrate synthase
  • E3 ubiquitin ligase complex SCF subunit
  • F-box protein UCC1
KeywordsTRANSFERASE/LIGASE / F-box protein / glyoxylate cycle / E3 ubiquitin ligase / LIGASE / 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: 2.3 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)168,5078
Polymers168,1384
Non-polymers3684
Water4,396244
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.589, 150.942, 160.286
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 55.93 %
Description: The entry contains friedel pairs in I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 200 mM Na acetate, 100 mM Na citrate pH 5.5, 10% (w/v) PEG 4000

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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: Nov 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→37.71 Å / Num. obs: 84031 / % possible obs: 99.63 % / Redundancy: 5.3 % / Biso Wilson estimate: 39.95 Å2 / CC1/2: 0.998 / Net I/σ(I): 21.9
Reflection shellResolution: 2.3→2.382 Å / Mean I/σ(I) obs: 3.28 / Num. unique obs: 8307 / CC1/2: 0.772

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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: 2.3→37.71 Å / SU ML: 0.2521 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.8254
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: The entry contains friedel pairs in I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2323 3810 2.37 %
Rwork0.2065 156751 -
obs0.2071 84023 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.31 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10481 0 24 244 10749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001610756
X-RAY DIFFRACTIONf_angle_d0.430214580
X-RAY DIFFRACTIONf_chiral_restr0.03751591
X-RAY DIFFRACTIONf_plane_restr0.00331866
X-RAY DIFFRACTIONf_dihedral_angle_d11.47693990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.320.35021520.31345489X-RAY DIFFRACTION93.64
2.32-2.350.30991280.30795853X-RAY DIFFRACTION99.15
2.35-2.390.32141330.29175781X-RAY DIFFRACTION99.31
2.39-2.420.31291530.28285864X-RAY DIFFRACTION99.29
2.42-2.460.31281390.27945824X-RAY DIFFRACTION99.18
2.46-2.50.34341490.26635873X-RAY DIFFRACTION99.39
2.5-2.540.29141110.25785861X-RAY DIFFRACTION99.22
2.54-2.580.26211460.25485810X-RAY DIFFRACTION99.35
2.58-2.630.25121460.25235811X-RAY DIFFRACTION99.2
2.63-2.680.24941440.24045819X-RAY DIFFRACTION99.07
2.68-2.730.27551490.24875789X-RAY DIFFRACTION99.13
2.73-2.790.26991530.23995844X-RAY DIFFRACTION99.27
2.79-2.860.27221200.23355868X-RAY DIFFRACTION99.27
2.86-2.930.24211680.22835838X-RAY DIFFRACTION99.39
2.93-3.010.25771300.22085807X-RAY DIFFRACTION99.56
3.01-3.10.26811390.23275890X-RAY DIFFRACTION99.37
3.1-3.20.27921270.22465851X-RAY DIFFRACTION99.47
3.2-3.310.24551540.22625798X-RAY DIFFRACTION99.17
3.31-3.440.2511380.21435841X-RAY DIFFRACTION99.27
3.44-3.60.26191360.20425846X-RAY DIFFRACTION99.04
3.6-3.790.23641500.19325800X-RAY DIFFRACTION98.94
3.79-4.030.21361480.1795816X-RAY DIFFRACTION98.89
4.03-4.340.19061390.16475860X-RAY DIFFRACTION99.27
4.34-4.770.16851390.16065797X-RAY DIFFRACTION99.18
4.77-5.460.17671410.17055822X-RAY DIFFRACTION99.22
5.46-6.870.22521420.19075844X-RAY DIFFRACTION99.32
6.87-37.710.17261360.17055455X-RAY DIFFRACTION92.8

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