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- PDB-1nex: Crystal Structure of ScSkp1-ScCdc4-CPD peptide complex -

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Basic information

Entry
Database: PDB / ID: 1nex
TitleCrystal Structure of ScSkp1-ScCdc4-CPD peptide complex
Components
  • CDC4 protein
  • Centromere DNA-binding protein complex CBF3 subunit D
  • GLL(TPO)PPQSG
KeywordsLIGASE / CELL CYCLE / WD 40 domain / phospho-peptide complex / E3 ubiquitin ligase
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
Cell division control protein 4 / Suppressor of kinetochore protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsOrlicky, S. / Tang, X. / Willems, A. / Tyers, M. / Sicheri, F.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2003
Title: Structural Basis for Phosphodependent Substrate Selection and Orientation by the SCFCdc4 Ubiquitin Ligase
Authors: Orlicky, S. / Tang, X. / Willems, A. / Tyers, M. / Sicheri, F.
History
DepositionDec 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 999 SEQUENCE Residues 36-63 have been deleted from chains A and C (Swiss-Prot accession P52286). ... SEQUENCE Residues 36-63 have been deleted from chains A and C (Swiss-Prot accession P52286). Residues 601-604 and 609-624 have been deleted from chains B and D (GenBank accession CAA29113, 3503). Also, residue 608 in chains B and D has been mutated from Cys608 to Leu608.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Centromere DNA-binding protein complex CBF3 subunit D
B: CDC4 protein
C: Centromere DNA-binding protein complex CBF3 subunit D
D: CDC4 protein
E: GLL(TPO)PPQSG
F: GLL(TPO)PPQSG


Theoretical massNumber of molelcules
Total (without water)147,6636
Polymers147,6636
Non-polymers00
Water1,29772
1
A: Centromere DNA-binding protein complex CBF3 subunit D
B: CDC4 protein
E: GLL(TPO)PPQSG


Theoretical massNumber of molelcules
Total (without water)73,8313
Polymers73,8313
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-26 kcal/mol
Surface area26400 Å2
MethodPISA
2
C: Centromere DNA-binding protein complex CBF3 subunit D
D: CDC4 protein
F: GLL(TPO)PPQSG


Theoretical massNumber of molelcules
Total (without water)73,8313
Polymers73,8313
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-24 kcal/mol
Surface area26680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.669, 107.669, 168.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Centromere DNA-binding protein complex CBF3 subunit D / ScSkp1 / Suppressor of kinetochore protein 1


Mass: 19739.037 Da / Num. of mol.: 2 / Fragment: residues 36-63 deleted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CBF3D OR SKP1 OR YDR328C OR D9798.14 / Plasmid: pProEx HTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon plus / References: UniProt: P52286
#2: Protein CDC4 protein / ScCdc4


Mass: 53143.469 Da / Num. of mol.: 2 / Fragment: residues 601-604 and 609-624 deleted / Mutation: C608L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P07834
#3: Protein/peptide GLL(TPO)PPQSG


Mass: 948.954 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 3.81 Å3/Da / Density % sol: 67.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Ammonium Sulphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
210 mMHEPES1droppH7.5
3250 mM1dropNaCl
41 mMdithiothreitol1drop
50.1 MTris1reservoirpH8.5
61.5 Mammonium sulfate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-BM-D10.9798, 0.9800
SYNCHROTRONAPS 14-BM-C20.9
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDMar 16, 2002bent conical Si mirror (Rh couting), Bent Ge(111) monochromator
ADSC QUANTUM 42CCDMar 16, 2002Si(111) double crystal monochromator, Bent cylindrical Si mirror (Rh coating)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Bent conical Si mirror (Rh coating), Bent Ge(111) monochromatorMADMx-ray1
2Si(111) double crystal monochromator, Bent cylindrical Si mirror (Rh coating)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97981
20.981
30.91
ReflectionResolution: 2.7→20 Å / Num. all: 119546 / Num. obs: 113960 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 43.4 Å2
Reflection shellResolution: 2.7→2.8 Å / % possible all: 93.6
Reflection
*PLUS
Num. obs: 116218 / % possible obs: 97.7 % / Num. measured all: 298371 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 93.6 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.7→19.99 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.273 10079 8.8 %RANDOM
Rwork0.239 ---
all0.239 119546 --
obs0.239 113960 95.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.1969 Å2 / ksol: 0.340039 e/Å3
Displacement parametersBiso mean: 40.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å23.77 Å20 Å2
2---1.49 Å20 Å2
3---2.97 Å2
Refine analyzeLuzzati coordinate error free: 0.45 Å / Luzzati sigma a free: 0.52 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9363 0 0 72 9435
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.85
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.389 616 3.7 %
Rwork0.344 16203 -
obs--84.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5TPO.PARAM
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / Rfactor Rwork: 0.238
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0089
X-RAY DIFFRACTIONc_angle_deg1.42
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85

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