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- PDB-2qlv: Crystal structure of the heterotrimer core of the S. cerevisiae A... -

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Basic information

Entry
Database: PDB / ID: 2qlv
TitleCrystal structure of the heterotrimer core of the S. cerevisiae AMPK homolog SNF1
Components
  • Carbon catabolite derepressing protein kinase
  • Nuclear protein SNF4
  • Protein SIP2
KeywordsTransferase/Protein binding / heterotrimer / ATP-binding / Carbohydrate metabolism / Kinase / Membrane / Nucleotide-binding / Nucleus / Phosphorylation / Serine/threonine-protein kinase / Transferase / Lipoprotein / Myristate / CBS domain / Transcription / Transcription regulation / Transferase-Protein binding COMPLEX
Function / homology
Function and homology information


fungal-type cell wall assembly / positive regulation of pseudohyphal growth / positive regulation of filamentous growth of a population of unicellular organisms in response to starvation / AMPK inhibits chREBP transcriptional activation activity / Energy dependent regulation of mTOR by LKB1-AMPK / single-species surface biofilm formation / regulation of cellular response to glucose starvation / regulation of invasive growth in response to glucose limitation / cellular bud neck septin ring / Carnitine metabolism ...fungal-type cell wall assembly / positive regulation of pseudohyphal growth / positive regulation of filamentous growth of a population of unicellular organisms in response to starvation / AMPK inhibits chREBP transcriptional activation activity / Energy dependent regulation of mTOR by LKB1-AMPK / single-species surface biofilm formation / regulation of cellular response to glucose starvation / regulation of invasive growth in response to glucose limitation / cellular bud neck septin ring / Carnitine metabolism / invasive growth in response to glucose limitation / peroxisome organization / Macroautophagy / filamentous growth / protein kinase regulator activity / nucleotide-activated protein kinase complex / enzyme-substrate adaptor activity / vacuolar membrane / AMP-activated protein kinase activity / nuclear envelope lumen / AMP binding / establishment of mitotic spindle orientation / positive regulation of macroautophagy / regulation of protein-containing complex assembly / response to unfolded protein / cellular response to glucose starvation / positive regulation of gluconeogenesis / response to endoplasmic reticulum stress / protein serine/threonine kinase activator activity / guanyl-nucleotide exchange factor activity / molecular function activator activity / autophagy / nuclear membrane / negative regulation of translation / non-specific serine/threonine protein kinase / carbohydrate metabolic process / protein kinase activity / intracellular signal transduction / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / regulation of transcription by RNA polymerase II / protein kinase binding / signal transduction / mitochondrion / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
N-terminal domain of TfIIb - #290 / Carbon catabolite-derepressing protein kinase, ubiquitin-associated domain / Ubiquitin associated domain (UBA) / Kinase associated domain 1, KA1 / Association with the SNF1 complex (ASC) domain / ASC domain superfamily / 5'-AMP-activated protein kinase beta subunit, interaction domain / 5'-AMP-activated protein kinase beta subunit, interation domain / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase ...N-terminal domain of TfIIb - #290 / Carbon catabolite-derepressing protein kinase, ubiquitin-associated domain / Ubiquitin associated domain (UBA) / Kinase associated domain 1, KA1 / Association with the SNF1 complex (ASC) domain / ASC domain superfamily / 5'-AMP-activated protein kinase beta subunit, interaction domain / 5'-AMP-activated protein kinase beta subunit, interation domain / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / AMP-activated protein kinase, glycogen-binding domain / Glycogen recognition site of AMP-activated protein kinase / CBS-domain / CBS-domain / KA1 domain/Ssp2, C-terminal / TATA-Binding Protein / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / N-terminal domain of TfIIb / CBS domain / CBS domain / CBS domain profile. / Single Sheet / Immunoglobulin E-set / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Immunoglobulins / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Carbon catabolite-derepressing protein kinase / 5'-AMP-activated protein kinase subunit gamma / SNF1 protein kinase subunit beta-2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAmodeo, G.A. / Rudolph, M.J. / Tong, L.
CitationJournal: Nature / Year: 2007
Title: Crystal structure of the heterotrimer core of Saccharomyces cerevisiae AMPK homologue SNF1.
Authors: Amodeo, G.A. / Rudolph, M.J. / Tong, L.
History
DepositionJul 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbon catabolite derepressing protein kinase
B: Protein SIP2
C: Nuclear protein SNF4
D: Carbon catabolite derepressing protein kinase
E: Protein SIP2
F: Nuclear protein SNF4


Theoretical massNumber of molelcules
Total (without water)168,3566
Polymers168,3566
Non-polymers00
Water2,000111
1
A: Carbon catabolite derepressing protein kinase
B: Protein SIP2
C: Nuclear protein SNF4


Theoretical massNumber of molelcules
Total (without water)84,1783
Polymers84,1783
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: Carbon catabolite derepressing protein kinase
E: Protein SIP2
F: Nuclear protein SNF4


Theoretical massNumber of molelcules
Total (without water)84,1783
Polymers84,1783
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.330, 81.840, 174.740
Angle α, β, γ (deg.)90.000, 102.220, 90.000
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is that of a trimer consisting of Snf1, Sip2, and Snf4.

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Components

#1: Protein Carbon catabolite derepressing protein kinase


Mass: 19596.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SNF1, CAT1, CCR1, GLC2, PAS14 / Plasmid: pET 28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: P06782, non-specific serine/threonine protein kinase
#2: Protein Protein SIP2 / Protein SPM2


Mass: 28956.588 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SIP2, SPM2 / Plasmid: pET 28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P34164
#3: Protein Nuclear protein SNF4 / Regulatory protein CAT3


Mass: 35625.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SNF4, CAT3 / Plasmid: pET 28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P12904
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 250 mM ammonium citrate, 15% PEG3350, 1mM AMP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2007
RadiationMonochromator: Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionRedundancy: 2.9 % / Av σ(I) over netI: 17.4 / Number: 130084 / Rmerge(I) obs: 0.071 / Χ2: 1.02 / D res high: 2.6 Å / D res low: 30 Å / Num. obs: 44415 / % possible obs: 93.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.593098.110.0470.9663.5
4.445.5998.810.0581.033.2
3.884.4497.910.0661.0123.1
3.533.8897.510.0911.0123.1
3.283.5397.810.121.0363.1
3.083.289810.1681.053
2.933.0897.510.2420.9822.8
2.82.9392.710.2891.0742.6
2.692.883.410.3430.9892.4
2.62.6971.310.3851.0752.1
ReflectionResolution: 2.6→30 Å / Num. obs: 44415 / % possible obs: 93.3 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.071 / Χ2: 1.018 / Net I/σ(I): 17.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.385 / Num. unique all: 3361 / Χ2: 1.075 / % possible all: 71.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
CBASSdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→29.54 Å / Rfactor Rfree error: 0.005 / FOM work R set: 0.727 / Data cutoff high absF: 501624.375 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.3
RfactorNum. reflection% reflectionSelection details
Rfree0.299 3208 7.6 %RANDOM
Rwork0.239 ---
obs-42058 88.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.919 Å2 / ksol: 0.311 e/Å3
Displacement parametersBiso mean: 66.3 Å2
Baniso -1Baniso -2Baniso -3
1--14.43 Å20 Å23.6 Å2
2---7.75 Å20 Å2
3---22.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9468 0 0 111 9579
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.661.5
X-RAY DIFFRACTIONc_mcangle_it2.922
X-RAY DIFFRACTIONc_scbond_it2.062
X-RAY DIFFRACTIONc_scangle_it3.282.5
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.403 230 8.6 %
Rwork0.369 2445 -
obs-2675 56.2 %
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

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