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- PDB-4lpa: Crystal structure of a Cdc6 phosphopeptide in complex with Cks1 -

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Basic information

Entry
Database: PDB / ID: 4lpa
TitleCrystal structure of a Cdc6 phosphopeptide in complex with Cks1
ComponentsCyclin-dependent kinases regulatory subunit
KeywordsPROTEIN BINDING / TRANSFERASE REGULATOR / Phospho-protein
Function / homology
Function and homology information


regulation of cell cycle G1/S phase transition / cyclin-dependent protein serine/threonine kinase activator activity / SCF ubiquitin ligase complex / protein kinase activator activity / cyclin-dependent protein kinase holoenzyme complex / regulation of mitotic cell cycle / ubiquitin binding / histone binding / cell division / regulation of transcription by RNA polymerase II ...regulation of cell cycle G1/S phase transition / cyclin-dependent protein serine/threonine kinase activator activity / SCF ubiquitin ligase complex / protein kinase activator activity / cyclin-dependent protein kinase holoenzyme complex / regulation of mitotic cell cycle / ubiquitin binding / histone binding / cell division / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Cyclin-Dependent Kinase Subunit Type 2 / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit superfamily / Cyclin-dependent kinase regulatory subunit / Cyclin-dependent kinases regulatory subunits signature 1. / Cyclin-dependent kinases regulatory subunits signature 2. / Cyclin-dependent kinase regulatory subunit / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cyclin-dependent kinases regulatory subunit
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMcGrath, D.A. / Balog, E.R.M. / Koivomagi, M. / Lucena, R. / Mai, M.V. / Hirschi, A. / Kellogg, D.R. / Loog, M. / Rubin, S.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Cks confers specificity to phosphorylation-dependent CDK signaling pathways.
Authors: McGrath, D.A. / Balog, E.R. / Koivomagi, M. / Lucena, R. / Mai, M.V. / Hirschi, A. / Kellogg, D.R. / Loog, M. / Rubin, S.M.
History
DepositionJul 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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_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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclin-dependent kinases regulatory subunit
B: Cyclin-dependent kinases regulatory subunit
C: Cyclin-dependent kinases regulatory subunit
D: Cyclin-dependent kinases regulatory subunit


Theoretical massNumber of molelcules
Total (without water)57,0484
Polymers57,0484
Non-polymers00
Water93752
1
A: Cyclin-dependent kinases regulatory subunit


Theoretical massNumber of molelcules
Total (without water)14,2621
Polymers14,2621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclin-dependent kinases regulatory subunit


Theoretical massNumber of molelcules
Total (without water)14,2621
Polymers14,2621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cyclin-dependent kinases regulatory subunit


Theoretical massNumber of molelcules
Total (without water)14,2621
Polymers14,2621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cyclin-dependent kinases regulatory subunit


Theoretical massNumber of molelcules
Total (without water)14,2621
Polymers14,2621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Cyclin-dependent kinases regulatory subunit
B: Cyclin-dependent kinases regulatory subunit

C: Cyclin-dependent kinases regulatory subunit
D: Cyclin-dependent kinases regulatory subunit


Theoretical massNumber of molelcules
Total (without water)57,0484
Polymers57,0484
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_454y-1/2,-x+1/2,z-1/41
Buried area5950 Å2
ΔGint-49 kcal/mol
Surface area25350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.690, 84.690, 239.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Cyclin-dependent kinases regulatory subunit / Cell division control protein CKS1


Mass: 14261.974 Da / Num. of mol.: 4
Fragment: Cyclin-dependent kinases regulatory subunit (unp residues 1-113)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CKS1, YBR1011, YBR135W / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20486
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 3.77 Å3/Da / Density % sol: 67.38 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 400mM potassium sodium tartrate, 0.1M MES, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 5, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.9→59.98 Å / Num. all: 20290 / Num. obs: 20254 / % possible obs: 99.79 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.0463 / Net I/σ(I): 12.65
Reflection shellResolution: 2.9→3.004 Å / Rmerge(I) obs: 0.2598 / Mean I/σ(I) obs: 3.57 / % possible all: 99.9

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALEITdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QB3

1qb3


Resolution: 2.9→58.147 Å / SU ML: 0.43 / σ(F): 1.36 / Phase error: 31.86 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2814 1993 9.9 %
Rwork0.2448 --
obs0.2485 20140 99.59 %
all-20290 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→58.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3772 0 0 52 3824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113916
X-RAY DIFFRACTIONf_angle_d1.3885332
X-RAY DIFFRACTIONf_dihedral_angle_d16.2041480
X-RAY DIFFRACTIONf_chiral_restr0.058552
X-RAY DIFFRACTIONf_plane_restr0.009692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9002-2.97270.37921370.32511257X-RAY DIFFRACTION100
2.9727-3.05310.32511410.33431275X-RAY DIFFRACTION100
3.0531-3.14290.38781380.31921263X-RAY DIFFRACTION99
3.1429-3.24430.33981390.29021258X-RAY DIFFRACTION99
3.2443-3.36030.30981380.27741262X-RAY DIFFRACTION100
3.3603-3.49480.31881400.26431269X-RAY DIFFRACTION100
3.4948-3.65380.28651400.25381276X-RAY DIFFRACTION100
3.6538-3.84640.2841440.24221303X-RAY DIFFRACTION100
3.8464-4.08740.28461370.23561276X-RAY DIFFRACTION100
4.0874-4.40290.26051430.20231290X-RAY DIFFRACTION100
4.4029-4.84580.22961430.18941300X-RAY DIFFRACTION99
4.8458-5.54650.22691460.21291325X-RAY DIFFRACTION100
5.5465-6.98610.30781480.26621343X-RAY DIFFRACTION100
6.9861-58.15860.25261590.24441450X-RAY DIFFRACTION100

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