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- PDB-4krc: Crystal Structure of Pho85-Pcl10-ATP-gamma-S Complex -

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Basic information

Entry
Database: PDB / ID: 4krc
TitleCrystal Structure of Pho85-Pcl10-ATP-gamma-S Complex
Components
  • Cyclin-dependent protein kinase PHO85
  • PHO85 cyclin-10
KeywordsTransferase/Signaling Protein / Glycogen Synthesis / Glycogen Synthesis Regulation / Transferase-Signaling Protein complex
Function / homology
Function and homology information


establishment or maintenance of cytoskeleton polarity / Pho85-Pho80 CDK-cyclin complex / negative regulation of phosphate metabolic process / regulation of establishment or maintenance of cell polarity / negative regulation of calcium-mediated signaling / regulation of cell cycle phase transition / long-chain fatty acid metabolic process / positive regulation of phospholipid biosynthetic process / fungal-type cell wall organization / regulation of glycogen biosynthetic process ...establishment or maintenance of cytoskeleton polarity / Pho85-Pho80 CDK-cyclin complex / negative regulation of phosphate metabolic process / regulation of establishment or maintenance of cell polarity / negative regulation of calcium-mediated signaling / regulation of cell cycle phase transition / long-chain fatty acid metabolic process / positive regulation of phospholipid biosynthetic process / fungal-type cell wall organization / regulation of glycogen biosynthetic process / regulation of nucleocytoplasmic transport / negative regulation of glycogen biosynthetic process / cell cycle G1/S phase transition / cellular bud neck / cyclin-dependent protein serine/threonine kinase regulator activity / negative regulation of macroautophagy / glycogen metabolic process / regulation of cell division / lipid homeostasis / positive regulation of macroautophagy / regulation of lipid metabolic process / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / G1/S transition of mitotic cell cycle / regulation of protein stability / regulation of protein localization / regulation of cell cycle / protein kinase activity / phosphorylation / protein serine kinase activity / DNA damage response / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / negative regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytoplasm
Similarity search - Function
Cyclin PHO80-like / Cyclin / Cyclin-like / Cyclin A; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Cyclin PHO80-like / Cyclin / Cyclin-like / Cyclin A; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Cyclin-dependent protein kinase PHO85 / PHO85 cyclin-10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.597 Å
AuthorsQuiocho, F.A. / Zheng, F.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: New Structural Insights into Phosphorylation-free Mechanism for Full Cyclin-dependent Kinase (CDK)-Cyclin Activity and Substrate Recognition.
Authors: Zheng, F. / Quiocho, F.A.
History
DepositionMay 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Nov 13, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Cyclin-dependent protein kinase PHO85
B: PHO85 cyclin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6574
Polymers60,1092
Non-polymers5482
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-32 kcal/mol
Surface area20330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.145, 65.378, 80.254
Angle α, β, γ (deg.)90.00, 100.61, 90.00
Int Tables number4
Space group name H-MP1211
DetailsHeterodimer is composed of one molecular Pho85 and one molecular Pcl10

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Components

#1: Protein Cyclin-dependent protein kinase PHO85 / Negative regulator of the PHO system / Serine/threonine-protein kinase PHO85


Mass: 36356.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: P7102.18A, PHO85, SSG3, YPL031C / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P17157, cyclin-dependent kinase
#2: Protein PHO85 cyclin-10


Mass: 23752.602 Da / Num. of mol.: 1 / Fragment: UNP residues 227-433
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: G2838, PCL10, YGL134W / Plasmid: pSBET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P53124
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 22-25% Polyethylene glycol 5000 monomethyl ether (PEG 5K MME), 0.1 M 2-morpholinoethanesulfonic acid (MES), pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97925 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 5, 2007
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.597→39.441 Å / Num. all: 15921 / Num. obs: 15166 / % possible obs: 95.26 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.41 / % possible all: 73.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.597→39.441 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2704 756 4.98 %random
Rwork0.2039 ---
obs0.2074 15166 95.26 %-
all-15921 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.393 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.4112 Å2-0 Å2-14.0521 Å2
2---12.6379 Å20 Å2
3---5.2267 Å2
Refinement stepCycle: LAST / Resolution: 2.597→39.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3528 0 32 23 3583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063630
X-RAY DIFFRACTIONf_angle_d0.9664957
X-RAY DIFFRACTIONf_dihedral_angle_d19.061245
X-RAY DIFFRACTIONf_chiral_restr0.059596
X-RAY DIFFRACTIONf_plane_restr0.004623
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5972-2.79760.31271090.23392418X-RAY DIFFRACTION80
2.7976-3.07910.28941510.22832901X-RAY DIFFRACTION97
3.0791-3.52440.28661440.20933022X-RAY DIFFRACTION100
3.5244-4.43940.27291680.18323009X-RAY DIFFRACTION100
4.4394-39.44570.25291840.19793060X-RAY DIFFRACTION100
Refinement TLS params.

S33: -0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.16520.4113-0.2371.3119-0.72851.2150.0004-0.0054-0.03330.17130.0119-0.0566-0.1370.05270.3632-0.0153-0.01260.3455-0.00570.34533.0252-5.799434.4235
20.6294-0.03570.6950.63250.28460.91020.06270.1554-0.8256-0.01980.2351-0.29070.18020.41170.5539-00.01770.8157-0.230.824211.4464-15.5934.6551
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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