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

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Basic information

Entry
Database: PDB / ID: 2pmi
TitleStructure of the Pho85-Pho80 CDK-cyclin Complex of the Phosphate-responsive Signal Transduction Pathway with Bound ATP-gamma-S
Components
  • Cyclin-dependent protein kinase PHO85
  • PHO85 cyclin PHO80
KeywordsSIGNALING PROTEIN / TRANSFERASE/CELL CYCLE / cyclin-dependent kinase / cyclin / 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 glycogen biosynthetic process / regulation of cell cycle phase transition / long-chain fatty acid metabolic process / regulation of establishment or maintenance of cell polarity / positive regulation of phospholipid biosynthetic process / vacuole fusion, non-autophagic / fungal-type cell wall organization ...establishment or maintenance of cytoskeleton polarity / Pho85-Pho80 CDK-cyclin complex / negative regulation of phosphate metabolic process / regulation of glycogen biosynthetic process / regulation of cell cycle phase transition / long-chain fatty acid metabolic process / regulation of establishment or maintenance of cell polarity / positive regulation of phospholipid biosynthetic process / vacuole fusion, non-autophagic / fungal-type cell wall organization / regulation of nucleocytoplasmic transport / intracellular monoatomic cation homeostasis / negative regulation of glycogen biosynthetic process / cell cycle G1/S phase transition / cellular bud neck / negative regulation of calcium-mediated signaling / cyclin-dependent protein serine/threonine kinase regulator activity / negative regulation of macroautophagy / lipid homeostasis / regulation of cell division / regulation of lipid metabolic process / positive regulation of macroautophagy / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein kinase holoenzyme complex / G1/S transition of mitotic cell cycle / protein destabilization / regulation of protein stability / regulation of protein localization / protein kinase activity / regulation of cell cycle / 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 / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site ...Cyclin PHO80-like / Cyclin / Cyclin-like / Cyclin A; domain 1 / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 PHO80
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 15, 2012Group: Non-polymer description
Revision 1.3Aug 30, 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: 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)140,1757
Polymers139,2614
Non-polymers9143
Water00
1
A: Cyclin-dependent protein kinase PHO85
B: PHO85 cyclin PHO80
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3494
Polymers69,6302
Non-polymers7182
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
Unit cell
Length a, b, c (Å)146.592, 146.592, 212.848
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a heterodimer. The asymmetric unit is composed of two heterodimers. The coordinates contain both heterodimers in the asymmetric unit.

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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-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
#4: 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: 1

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Sample preparation

CrystalDensity Matthews: 4.74 Å3/Da / Density % sol: 74.04 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 9ul 12% PEG 10000, 10% glycerol, 0.05 M strontium chloride (SrCl2), 10 mM Tris (2-carboxyethyl) phosphine (TCEP, 0.1 M 2-morpholinoethanesulfonic acid (MES), pH 6.5, VAPOR DIFFUSION, HANGING ...Details: 9ul 12% PEG 10000, 10% glycerol, 0.05 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

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 4, 2006 / Details: APS 19ID
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.9→14.98 Å / Num. all: 53704 / Num. obs: 53704 / % possible obs: 91.1 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 11
Reflection shellResolution: 2.9→3 Å / Redundancy: 2 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.248 / % possible all: 75.6

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PK9

2pk9


Resolution: 2.9→14.98 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 97128.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.325 2707 5.1 %RANDOM
Rwork0.289 ---
obs0.289 53533 91.2 %-
all-53704 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.7203 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 49.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.9→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8083 0 55 0 8138
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.773
X-RAY DIFFRACTIONc_mcangle_it6.075
X-RAY DIFFRACTIONc_scbond_it5.275
X-RAY DIFFRACTIONc_scangle_it7.768
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 402 5.3 %
Rwork0.323 7163 -
obs--78.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2mes_xplor_par_a.txtmes_xplor_top.txt
X-RAY DIFFRACTION3sap_a.paramsap.top

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