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- PDB-2pk9: Structure of the Pho85-Pho80 CDK-cyclin Complex of the Phosphate-... -

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Basic information

Entry
Database: PDB / ID: 2pk9
TitleStructure of the Pho85-Pho80 CDK-cyclin Complex of the Phosphate-responsive Signal Transduction Pathway
Components
  • Cyclin-dependent protein kinase PHO85
  • PHO85 cyclin PHO80
KeywordsSIGNALING PROTEIN / TRANSFERASE/CELL CYCLE / cyclin-dependent kinase / cyclin / TRANSFERASE- CELL CYCLE COMPLEX / TRANSFERASE-CELL CYCLE 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 / vacuole fusion, non-autophagic / positive regulation of phospholipid biosynthetic process / fungal-type cell wall organization ...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 / vacuole fusion, non-autophagic / positive regulation of phospholipid biosynthetic process / fungal-type cell wall organization / regulation of glycogen biosynthetic process / regulation of nucleocytoplasmic transport / intracellular monoatomic cation homeostasis / negative regulation of glycogen biosynthetic process / cell cycle G1/S phase transition / cellular bud neck / cyclin-dependent protein serine/threonine kinase regulator activity / synaptic vesicle transport / negative regulation of macroautophagy / 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 / vesicle-mediated transport / regulation of protein stability / G1/S transition of mitotic cell cycle / regulation of protein localization / neuron apoptotic process / 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
Cyclin-dependent protein kinase PHO85 / PHO85 cyclin PHO80
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.906 Å
AuthorsHuang, K. / Ferrin-O'Connell, I. / Zhang, W. / Leonard, G.A. / O'Shea, E.K. / Quiocho, F.A.
CitationJournal: Mol.Cell / Year: 2007
Title: Structure of the Pho85-Pho80 CDK-Cyclin Complex of the Phosphate-Responsive Signal Transduction Pathway
Authors: Huang, K. / Ferrin-O'Connell, I. / Zhang, W. / Leonard, G.A. / O'Shea, E.K. / Quiocho, F.A.
History
DepositionApr 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Advisory / Data collection / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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
Remark 999 SEQUENCE SEQUENCE WARNING: RESIDUE (D GLN 16 ) AND RESIDUE (D GLY 17 ) ARE NOT LINKED. DISTANCE OF ... SEQUENCE SEQUENCE WARNING: RESIDUE (D GLN 16 ) AND RESIDUE (D GLY 17 ) ARE NOT LINKED. DISTANCE OF C-N BOND IS 2.46

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclin-dependent protein kinase PHO85
B: PHO85 cyclin PHO80
C: Cyclin-dependent protein kinase PHO85
D: PHO85 cyclin PHO80
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,6516
Polymers139,2614
Non-polymers3902
Water00
1
A: Cyclin-dependent protein kinase PHO85
B: PHO85 cyclin PHO80
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8263
Polymers69,6302
Non-polymers1951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Cyclin-dependent protein kinase PHO85
D: PHO85 cyclin PHO80
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8263
Polymers69,6302
Non-polymers1951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.775, 147.775, 211.825
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Cyclin-dependent protein kinase PHO85 / E.C.2.7.11.22 / Serine/threonine-protein kinase PHO85 / Negative regulator of the PHO system


Mass: 36356.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PHO85, SSG3 / Plasmid: pQE60 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P17157, cyclin-dependent kinase
#2: Protein PHO85 cyclin PHO80 / Phosphate system cyclin PHO80 / Aminoglycoside antibiotic sensitivity protein 3


Mass: 33273.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PHO80, AGS3, TUP7, VAC5 / Plasmid: pSBET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P20052
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.79 Å3/Da / Density % sol: 74.33 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 9ul 12% PEG 10000, 10% glycerol, 0.2ul 0.25 M strontium chloride (SrCl2), 10 mM Tris (2-carboxyethyl) phosphine (TCEP, 0.1 M 2-morpholinoethanesulfonic acid (MES), pH 6.5, VAPOR DIFFUSION, ...Details: 9ul 12% PEG 10000, 10% glycerol, 0.2ul 0.25 M strontium chloride (SrCl2), 10 mM Tris (2-carboxyethyl) phosphine (TCEP, 0.1 M 2-morpholinoethanesulfonic acid (MES), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12001
22001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97948
SYNCHROTRONESRF ID2920.97926
Detector
TypeIDDetectorDateDetails
CUSTOM-MADE1CCDJul 21, 2005APS 19ID
ADSC QUANTUM 3152CCDApr 11, 2005ESRF ID29
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979481
20.979261
ReflectionResolution: 2.906→15.03 Å / Num. all: 52156 / Num. obs: 47431 / % possible obs: 88.4 % / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 12.2
Reflection shellResolution: 2.906→3 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.29 / % possible all: 71.2

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Processing

Software
NameVersionClassification
REFMAC5.2refinement
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 2.906→15.03 Å / Cor.coef. Fo:Fc: 0.862 / Cor.coef. Fo:Fc free: 0.819 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.575 / ESU R Free: 0.388 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31536 2622 5 %RANDOM
Rwork0.28146 ---
obs0.28316 49532 88.49 %-
all-52156 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.804 Å2
Baniso -1Baniso -2Baniso -3
1-5.14 Å22.57 Å20 Å2
2--5.14 Å20 Å2
3----7.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.906→15.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7994 0 24 0 8018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228055
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.97510916
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5155970
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.74723.704351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.716151400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5691549
X-RAY DIFFRACTIONr_chiral_restr0.1150.21248
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025975
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.23689
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.25433
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2217
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.091.54921
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33427969
X-RAY DIFFRACTIONr_scbond_it0.72333134
X-RAY DIFFRACTIONr_scangle_it1.2374.52947
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.906→2.979 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 161 -
Rwork0.36 2749 -
obs--70.07 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2mes_xplor_par_a.txt

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