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- PDB-3mks: Crystal Structure of yeast Cdc4/Skp1 in complex with an allosteri... -

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Basic information

Entry
Database: PDB / ID: 3mks
TitleCrystal Structure of yeast Cdc4/Skp1 in complex with an allosteric inhibitor SCF-I2
Components
  • Cell division control protein 4
  • Suppressor of kinetochore protein 1
KeywordsLIGASE/CELL CYCLE / ubiquitin ligase / protein binding / small molecule complex / LIGASE-CELL CYCLE complex
Function / homology
Function and homology information


nuclear SCF ubiquitin ligase complex / RAVE complex / Iron uptake and transport / CBF3 complex / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / vacuolar proton-transporting V-type ATPase complex assembly / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / septin ring assembly ...nuclear SCF ubiquitin ligase complex / RAVE complex / Iron uptake and transport / CBF3 complex / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / vacuolar proton-transporting V-type ATPase complex assembly / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / septin ring assembly / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of exit from mitosis / Antigen processing: Ubiquitination & Proteasome degradation / vacuolar acidification / kinetochore assembly / regulation of metabolic process / exit from mitosis / positive regulation of glucose transmembrane transport / protein neddylation / mitotic intra-S DNA damage checkpoint signaling / U3 snoRNA binding / silent mating-type cassette heterochromatin formation / mitochondrial fusion / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / sporulation resulting in formation of a cellular spore / DNA replication origin binding / 90S preribosome / regulation of mitotic cell cycle / cullin family protein binding / subtelomeric heterochromatin formation / regulation of protein-containing complex assembly / phosphoserine residue binding / endomembrane system / negative regulation of cytoplasmic translation / meiotic cell cycle / ubiquitin binding / G1/S transition of mitotic cell cycle / kinetochore / nuclear matrix / G2/M transition of mitotic cell cycle / mitotic cell cycle / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / chromosome, telomeric region / protein ubiquitination / cell division / nucleolus / nucleus / cytoplasm
Similarity search - Function
Cell division control protein 4, dimerisation domain / Cell division control protein 4 dimerisation domain / F-box domain / Monooxygenase - #50 / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like / SKP1 component, dimerisation / S-phase kinase-associated protein 1 ...Cell division control protein 4, dimerisation domain / Cell division control protein 4 dimerisation domain / F-box domain / Monooxygenase - #50 / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Monooxygenase / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / SKP1/BTB/POZ domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,1'-binaphthalene-2,2'-dicarboxylic acid / Cell division control protein 4 / Suppressor of kinetochore protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsOrlicky, S. / Sicheri, F. / Tyers, M. / Tang, X.
CitationJournal: Nat.Biotechnol. / Year: 2010
Title: An allosteric inhibitor of substrate recognition by the SCF(Cdc4) ubiquitin ligase.
Authors: Orlicky, S. / Tang, X. / Neduva, V. / Elowe, N. / Brown, E.D. / Sicheri, F. / Tyers, M.
History
DepositionApr 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Suppressor of kinetochore protein 1
B: Cell division control protein 4
C: Suppressor of kinetochore protein 1
D: Cell division control protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,22417
Polymers144,7334
Non-polymers1,49113
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Suppressor of kinetochore protein 1
B: Cell division control protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8477
Polymers72,3672
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-88 kcal/mol
Surface area27380 Å2
MethodPISA
3
C: Suppressor of kinetochore protein 1
D: Cell division control protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,37710
Polymers72,3672
Non-polymers1,0118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-84 kcal/mol
Surface area27250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.281, 108.281, 165.594
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Suppressor of kinetochore protein 1 / Centromere DNA-binding protein complex CBF3 subunit D / E3 ubiquitin ligase complex SCF subunit SKP1


Mass: 19504.561 Da / Num. of mol.: 2 / Fragment: UNP Residues 2-194 with 37-64 deleted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SKP1, CBF3D, YDR328C, D9798.14 / Plasmid: pProEx / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon plus / References: UniProt: P52286
#2: Protein Cell division control protein 4 / F-box protein CDC4 / E3 ubiquitin ligase complex SCF subunit CDC4


Mass: 52862.098 Da / Num. of mol.: 2
Fragment: UNP Residues 263-744 with 602-605 and 609-624 deleted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CDC4, YFL009W / Plasmid: pProEx / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon plus / References: UniProt: P07834

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Non-polymers , 4 types, 53 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-C1C / 1,1'-binaphthalene-2,2'-dicarboxylic acid / 1-(2-carboxynaphth-1yl)-2-naphthoic acid


Mass: 342.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H14O4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE UNIPROT ENTRY FOR CDC4_YEAST INDICATES THAT K460E EXISTS AS A CONFLICT AND IS PRESENT IN THIS ENTRY

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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: 3.87 Å3/Da / Density % sol: 68.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.5 M Ammonium sulfate, 100mM Tris pH 8.5, 15% glycerol, 1mM SCF-I2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 12, 2004
Details: Si(111) double crystal monochromator, Bent cylindrical Si mirror (Rh coating)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionNumber: 374289 / Rmerge(I) obs: 0.058 / Χ2: 0.99 / D res high: 2.6 Å / D res low: 30 Å / Num. obs: 66680 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
5.593098.310.0330.769
4.445.5910010.0290.446
3.884.4410010.0380.729
3.533.8810010.0591.028
3.283.5310010.0781.113
3.083.2810010.111.248
2.933.0810010.181.292
2.82.9310010.2411.162
2.692.810010.3291.049
2.62.6910010.4351.029
ReflectionResolution: 2.6→93.66 Å / Num. all: 66846 / Num. obs: 66846 / % possible obs: 99.8 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 24.3
Reflection shellResolution: 2.6→2.688 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRMethod rotation: fast direct / Method translation: &STRIP%trans_method

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
CNSrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NEX

1nex


Resolution: 2.6→93.66 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.894 / SU B: 21.478 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.34 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26648 3375 5.1 %RANDOM
Rwork0.21058 ---
obs0.21334 63268 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.854 Å2
Baniso -1Baniso -2Baniso -3
1-1.86 Å20.93 Å20 Å2
2--1.86 Å20 Å2
3----2.79 Å2
Refinement stepCycle: LAST / Resolution: 2.6→93.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9329 0 87 40 9456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0229605
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9681.95413003
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.46851145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31823.781447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.01151700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.371563
X-RAY DIFFRACTIONr_chiral_restr0.1260.21448
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217133
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7841.55735
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.47929306
X-RAY DIFFRACTIONr_scbond_it2.42233870
X-RAY DIFFRACTIONr_scangle_it3.8364.53697
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 241 -
Rwork0.301 4731 -
obs--100 %
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)
12.1411-1.0844-0.84849.11065.6656.84850.1236-0.0570.18440.4072-0.08360.03870.24460.1441-0.040.4125-0.0359-0.16880.0807-0.0440.1738113.4496-29.4947-58.3148
20.9292-0.28550.19372.63240.28451.53790.12170.16780.1622-0.1278-0.0482-0.4416-0.17590.3553-0.07340.0473-0.02680.06060.206-0.01420.1839118.901117.1824-62.3966
32.73132.4582.44984.35552.7485.5958-0.17020.38120.0062-0.4570.2319-0.1098-0.19450.1945-0.06160.05540.00360.01440.21030.0290.0404139.318713.369-30.3781
42.7421-0.2725-0.98870.07880.18041.2295-0.0002-0.35590.06490.01820.0084-0.0488-0.08240.1768-0.00820.05630.0009-0.02670.08520.01860.0511182.451727.7759-35.5226
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 185
2X-RAY DIFFRACTION2B270 - 744
3X-RAY DIFFRACTION3C4 - 186
4X-RAY DIFFRACTION4D269 - 744

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