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- PDB-3mn3: An inhibited conformation for the protein kinase domain of the Sa... -

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Basic information

Entry
Database: PDB / ID: 3mn3
TitleAn inhibited conformation for the protein kinase domain of the Saccharomyces cerevisiae AMPK homolog Snf1
ComponentsCarbon catabolite-derepressing protein kinase
KeywordsTRANSFERASE / SNF1 / kinase domain / autoinhibitory region
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 / Macroautophagy / filamentous growth / nucleotide-activated protein kinase complex / vacuolar membrane / AMP-activated protein kinase activity / nuclear envelope lumen / establishment of mitotic spindle orientation / positive regulation of macroautophagy / response to unfolded protein / positive regulation of gluconeogenesis / response to endoplasmic reticulum stress / guanyl-nucleotide exchange factor activity / molecular function activator activity / nuclear membrane / negative regulation of translation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / mitochondrion / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Carbon catabolite-derepressing protein kinase, ubiquitin-associated domain / Ubiquitin associated domain (UBA) / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / KA1 domain/Ssp2, C-terminal / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site ...Carbon catabolite-derepressing protein kinase, ubiquitin-associated domain / Ubiquitin associated domain (UBA) / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / KA1 domain/Ssp2, C-terminal / 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
Carbon catabolite-derepressing protein kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsRudolph, M.J. / Amodeo, G.A. / Tong, L.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: An inhibited conformation for the protein kinase domain of the Saccharomyces cerevisiae AMPK homolog Snf1.
Authors: Rudolph, M.J. / Amodeo, G.A. / Tong, L.
History
DepositionApr 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 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

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Assembly

Deposited unit
A: Carbon catabolite-derepressing protein kinase


Theoretical massNumber of molelcules
Total (without water)31,0281
Polymers31,0281
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Carbon catabolite-derepressing protein kinase

A: Carbon catabolite-derepressing protein kinase


Theoretical massNumber of molelcules
Total (without water)62,0562
Polymers62,0562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_565-x,-y+1,z1
Buried area2610 Å2
ΔGint-19 kcal/mol
Surface area24360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.981, 76.981, 286.215
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Carbon catabolite-derepressing protein kinase


Mass: 31028.217 Da / Num. of mol.: 1 / Fragment: UNP residues 50-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SNF1, CAT1, CCR1, GLC2, PAS14, YDR477W, D8035.20 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)
References: UniProt: P06782, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.42 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7.5
Details: 10% (w/v) PEG3350 and 50mM Na2SO4, pH 7.5, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9815 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 1, 2009
RadiationMonochromator: horizontally deflecting and focusing crystal preceded by a vertically focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9815 Å / Relative weight: 1
ReflectionResolution: 2.38→30 Å / Num. all: 19910 / Num. obs: 19799 / % possible obs: 99 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 2.38→2.48 Å / % possible all: 99

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→30 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 1 / SU B: 15.093 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.286 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 872 5 %RANDOM
Rwork0.23 ---
obs0.231 17349 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.14 Å2 / Biso mean: 59.94 Å2 / Biso min: 40.67 Å2
Baniso -1Baniso -2Baniso -3
1-2.88 Å20 Å20 Å2
2--2.88 Å20 Å2
3----5.76 Å2
Refinement stepCycle: LAST / Resolution: 2.38→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 0 54 2094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222085
X-RAY DIFFRACTIONr_angle_refined_deg1.271.9772819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6055249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.14223.87193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.7615382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.351512
X-RAY DIFFRACTIONr_chiral_restr0.080.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021544
X-RAY DIFFRACTIONr_nbd_refined0.1960.2858
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21392
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.277
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.25
X-RAY DIFFRACTIONr_mcbond_it0.6151.51304
X-RAY DIFFRACTIONr_mcangle_it1.13322044
X-RAY DIFFRACTIONr_scbond_it1.2933892
X-RAY DIFFRACTIONr_scangle_it2.1054.5775
LS refinement shellResolution: 2.38→2.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 64 -
Rwork0.3 1139 -
all-1203 -
obs--96.09 %
Refinement TLS params.

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 °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8466-1.4269-0.70633.07320.40835.1587-0.08970.05040.45280.09880.26110.2069-0.5944-0.6458-0.1714-0.04280.05920.0172-0.06250.0434-0.1016-18.01733.836231.712
21.34730.3817-0.40182.3262-0.18772.7232-0.14880.13370.0294-0.02070.1864-0.15160.09410.0266-0.0376-0.1036-0.1521-0.038-0.0514-0.0326-0.1289-4.343622.2612.4289
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A50 - 135
2X-RAY DIFFRACTION2A136 - 320

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