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- PDB-6e4w: Structure of AMPK bound to activator -

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Basic information

Entry
Database: PDB / ID: 6e4w
TitleStructure of AMPK bound to activator
Components
  • (5'-AMP-activated protein kinase subunit ...) x 2
  • 5'-AMP-activated protein kinase catalytic subunit alpha-1
KeywordsTRANSFERASE / Kinase / AMPK / activator / allostery / TRANSFERASE-ACTIVATOR complex
Function / homology
Function and homology information


eukaryotic elongation factor-2 kinase activator activity / Energy dependent regulation of mTOR by LKB1-AMPK / Regulation of TP53 Activity through Phosphorylation / Macroautophagy / TP53 Regulates Metabolic Genes / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / positive regulation of mitochondrial transcription ...eukaryotic elongation factor-2 kinase activator activity / Energy dependent regulation of mTOR by LKB1-AMPK / Regulation of TP53 Activity through Phosphorylation / Macroautophagy / TP53 Regulates Metabolic Genes / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / positive regulation of mitochondrial transcription / negative regulation of tubulin deacetylation / histone H2BS36 kinase activity / cold acclimation / AMP-activated protein kinase activity / lipid droplet disassembly / phosphatidylethanolamine biosynthetic process / regulation of carbon utilization / positive regulation of skeletal muscle tissue development / CAMKK-AMPK signaling cascade / import into nucleus / phosphatidylcholine biosynthetic process / regulation of vesicle-mediated transport / negative regulation of T cell mediated immune response to tumor cell / protein localization to lysosome / negative regulation of hepatocyte apoptotic process / positive regulation of fatty acid oxidation / positive regulation of T cell mediated immune response to tumor cell / tau-protein kinase / protein K6-linked ubiquitination / nucleotide-activated protein kinase complex / regulation of vascular permeability / protein kinase regulator activity / negative regulation of TOR signaling / negative regulation of protein localization to nucleus / response to caffeine / regulation of glycolytic process / : / protein localization to lipid droplet / tau-protein kinase activity / lysosome organization / negative regulation of T cell activation / cellular response to stress / cholesterol biosynthetic process / lipid biosynthetic process / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / AMP binding / hepatocyte apoptotic process / fatty acid oxidation / TORC1 signaling / motor behavior / positive regulation of release of cytochrome c from mitochondria / positive regulation of translational initiation / cellular response to ethanol / fatty acid homeostasis / autophagosome assembly / negative regulation of lipid catabolic process / response to UV / cellular response to glucose starvation / energy homeostasis / positive regulation of protein localization / negative regulation of TORC1 signaling / positive regulation of adipose tissue development / negative regulation of translational initiation / positive regulation of TORC1 signaling / positive regulation of gluconeogenesis / negative regulation of insulin receptor signaling pathway / positive regulation of autophagy / cellular response to nutrient levels / cellular response to calcium ion / cellular response to amino acid starvation / positive regulation of glycolytic process / cellular response to starvation / regulation of microtubule cytoskeleton organization / response to activity / positive regulation of D-glucose import across plasma membrane / response to gamma radiation / protein localization to plasma membrane / circadian regulation of gene expression / response to hydrogen peroxide / cellular response to glucose stimulus / neuron cellular homeostasis / ADP binding / regulation of circadian rhythm / protein destabilization / response to estrogen / cellular response to xenobiotic stimulus / autophagy / glucose metabolic process / Wnt signaling pathway / cellular response to hydrogen peroxide / positive regulation of T cell activation / fatty acid biosynthetic process / glucose homeostasis / cellular response to prostaglandin E stimulus / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / protein-containing complex assembly / cellular response to hypoxia / proteasome-mediated ubiquitin-dependent protein catabolic process / protein phosphorylation
Similarity search - Function
PRKAA1, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase alpha 1 catalytic subunit, C-terminal / : / AMP-activated protein kinase, alpha subunit, autoinhibitory domain / : / 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 ...PRKAA1, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase alpha 1 catalytic subunit, C-terminal / : / AMP-activated protein kinase, alpha subunit, autoinhibitory domain / : / 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 / KA1 domain/Ssp2, C-terminal / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Immunoglobulin E-set / 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. / Immunoglobulin-like fold / 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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / Chem-HUG / STAUROSPORINE / 5'-AMP-activated protein kinase catalytic subunit alpha-1 / 5'-AMP-activated protein kinase subunit gamma-1 / 5'-AMP-activated protein kinase subunit beta-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.35 Å
AuthorsCalabrese, M.F. / Kurumbail, R.G.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Acyl Glucuronide Metabolites of 6-Chloro-5-[4-(1-hydroxycyclobutyl)phenyl]-1 H-indole-3-carboxylic Acid (PF-06409577) and Related Indole-3-carboxylic Acid Derivatives are Direct Activators of ...Title: Acyl Glucuronide Metabolites of 6-Chloro-5-[4-(1-hydroxycyclobutyl)phenyl]-1 H-indole-3-carboxylic Acid (PF-06409577) and Related Indole-3-carboxylic Acid Derivatives are Direct Activators of Adenosine Monophosphate-Activated Protein Kinase (AMPK).
Authors: Ryder, T.F. / Calabrese, M.F. / Walker, G.S. / Cameron, K.O. / Reyes, A.R. / Borzilleri, K.A. / Delmore, J. / Miller, R. / Kurumbail, R.G. / Ward, J. / Kung, D.W. / Brown, J.A. / Edmonds, D. ...Authors: Ryder, T.F. / Calabrese, M.F. / Walker, G.S. / Cameron, K.O. / Reyes, A.R. / Borzilleri, K.A. / Delmore, J. / Miller, R. / Kurumbail, R.G. / Ward, J. / Kung, D.W. / Brown, J.A. / Edmonds, D.J. / Eng, H. / Wolford, A.C. / Kalgutkar, A.S.
History
DepositionJul 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: 5'-AMP-activated protein kinase catalytic subunit alpha-1
B: 5'-AMP-activated protein kinase subunit beta-1
C: 5'-AMP-activated protein kinase subunit gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,63512
Polymers118,3103
Non-polymers2,3249
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12580 Å2
ΔGint-111 kcal/mol
Surface area36030 Å2
MethodPISA
2
A: 5'-AMP-activated protein kinase catalytic subunit alpha-1
B: 5'-AMP-activated protein kinase subunit beta-1
C: 5'-AMP-activated protein kinase subunit gamma-1
hetero molecules

A: 5'-AMP-activated protein kinase catalytic subunit alpha-1
B: 5'-AMP-activated protein kinase subunit beta-1
C: 5'-AMP-activated protein kinase subunit gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,26924
Polymers236,6216
Non-polymers4,64818
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area28250 Å2
ΔGint-231 kcal/mol
Surface area68970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.970, 123.970, 402.120
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 5'-AMP-activated protein kinase catalytic subunit alpha-1 / AMPK subunit alpha-1 / Acetyl-CoA carboxylase kinase / ACACA kinase / Hydroxymethylglutaryl-CoA ...AMPK subunit alpha-1 / Acetyl-CoA carboxylase kinase / ACACA kinase / Hydroxymethylglutaryl-CoA reductase kinase / HMGCR kinase / Tau-protein kinase PRKAA1


Mass: 57779.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prkaa1, Ampk1 / Production host: Escherichia coli (E. coli)
References: UniProt: P54645, non-specific serine/threonine protein kinase, EC: 2.7.11.27, [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase, tau-protein kinase

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5'-AMP-activated protein kinase subunit ... , 2 types, 2 molecules BC

#2: Protein 5'-AMP-activated protein kinase subunit beta-1 / AMPKb / 5'-AMP-activated protein kinase 40 kDa subunit


Mass: 23097.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prkab1 / Production host: Escherichia coli (E. coli) / References: UniProt: P80386
#3: Protein 5'-AMP-activated protein kinase subunit gamma-1 / AMPKg


Mass: 37434.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prkag1 / Production host: Escherichia coli (E. coli) / References: UniProt: P80385

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Non-polymers , 6 types, 9 molecules

#4: Chemical ChemComp-STU / STAUROSPORINE


Mass: 466.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM
#5: Chemical ChemComp-HUG / 1-O-(4,6-difluoro-5-{4-[(2S)-oxan-2-yl]phenyl}-1H-indole-3-carbonyl)-beta-D-glucopyranuronic acid


Mass: 533.475 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H25F2NO9
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#8: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#9: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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Details

Has protein modificationY

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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: 3.86 Å3/Da / Density % sol: 68.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 750 MM AMMONIUM SULFATE, 500 MM LITHIUM SULFATE, 100 MM TRISODIUM CITRATE, 1% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→40.58 Å / Num. obs: 27326 / % possible obs: 100 % / Redundancy: 12.3 % / Biso Wilson estimate: 105.07 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 16.2
Reflection shellResolution: 3.35→3.47 Å / Rmerge(I) obs: 0.689 / Num. unique all: 2634

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER2.11.7refinement
PDB_EXTRACT3.24data extraction
autoXDSdata reduction
PHASERphasing
RefinementResolution: 3.35→40.58 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.866 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.576 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.101 / SU Rfree Blow DPI: 0.395 / SU Rfree Cruickshank DPI: 0.398
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1369 5.02 %RANDOM
Rwork0.209 ---
obs0.21 27267 99.9 %-
Displacement parametersBiso max: 243.42 Å2 / Biso mean: 113.76 Å2 / Biso min: 52.34 Å2
Baniso -1Baniso -2Baniso -3
1--13.3599 Å20 Å20 Å2
2---13.3599 Å20 Å2
3---26.7198 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: final / Resolution: 3.35→40.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6344 0 154 0 6498
Biso mean--132.71 --
Num. residues----799
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2277SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes133HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1005HARMONIC5
X-RAY DIFFRACTIONt_it6651HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion881SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7785SEMIHARMONIC0
X-RAY DIFFRACTIONt_bond_d6651HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9057HARMONIC21.27
X-RAY DIFFRACTIONt_omega_torsion2.71
X-RAY DIFFRACTIONt_other_torsion23.17
LS refinement shellResolution: 3.35→3.48 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.229 147 5.32 %
Rwork0.223 2616 -
all0.224 2763 -
obs--99.57 %
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)
10.3368-0.3587-0.0591.54520.94792.50960.041-0.03170.0298-0.2143-0.15520.1428-0.6411-0.34240.11410.37260.0604-0.06110.1465-0.17060.006229.3192-75.0726-16.4964
22.5619-0.8883-2.91230.05091.53354.7201-0.05930.13850.1757-0.11260.05320.2645-0.6466-0.37570.00610.47810.09180.04910.1549-0.16140.125235.1626-67.1069-31.0598
32.6125-2.03510.13524.44442.58394.95220.037-0.50340.6376-0.37110.594-0.5251-0.52090.6004-0.6311-0.00230.14020.15320.2049-0.34920.116122.1482-40.34516.6669
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A9 - 548
2X-RAY DIFFRACTION2{ B|* }B79 - 270
3X-RAY DIFFRACTION3{ C|* }C28 - 322

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