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- PDB-5ufu: Structure of AMPK bound to activator -

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Basic information

Entry
Database: PDB / ID: 5ufu
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/ACTIVATOR / Kinase / AMPK / activator / allostery / TRANSFERASE-ACTIVATOR complex
Function / homology
Function and homology information


bile acid signaling pathway / : / positive regulation of peptidyl-lysine acetylation / Energy dependent regulation of mTOR by LKB1-AMPK / eukaryotic elongation factor-2 kinase activator activity / regulation of bile acid secretion / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / Macroautophagy / regulation of peptidyl-serine phosphorylation / Energy dependent regulation of mTOR by LKB1-AMPK ...bile acid signaling pathway / : / positive regulation of peptidyl-lysine acetylation / Energy dependent regulation of mTOR by LKB1-AMPK / eukaryotic elongation factor-2 kinase activator activity / regulation of bile acid secretion / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / Macroautophagy / regulation of peptidyl-serine phosphorylation / Energy dependent regulation of mTOR by LKB1-AMPK / Regulation of TP53 Activity through Phosphorylation / negative regulation of tubulin deacetylation / Macroautophagy / TP53 Regulates Metabolic Genes / nail development / positive regulation of mitochondrial transcription / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / TP53 Regulates Metabolic Genes / histone H2BS36 kinase activity / cold acclimation / AMP-activated protein kinase activity / lipid droplet disassembly / regulation of catalytic activity / positive regulation of skeletal muscle tissue development / import into nucleus / CAMKK-AMPK signaling cascade / negative regulation of hepatocyte apoptotic process / regulation of vesicle-mediated transport / positive regulation of fatty acid oxidation / Regulation of TP53 Activity through Phosphorylation / positive regulation of T cell mediated immune response to tumor cell / tau-protein kinase / nucleotide-activated protein kinase complex / protein kinase regulator activity / regulation of vascular permeability / negative regulation of TOR signaling / protein localization to membrane / regulation of glycolytic process / : / protein localization to lipid droplet / response to caffeine / cholesterol biosynthetic process / tau-protein kinase activity / AMP binding / lipid biosynthetic process / cellular response to stress / bile acid and bile salt transport / fatty acid oxidation / motor behavior / negative regulation of ferroptosis / fatty acid homeostasis / cellular response to ethanol / negative regulation of lipid catabolic process / response to UV / energy homeostasis / cellular response to glucose starvation / positive regulation of protein localization / positive regulation of adipose tissue development / negative regulation of TORC1 signaling / negative regulation of insulin receptor signaling pathway / positive regulation of autophagy / cellular response to nutrient levels / positive regulation of gluconeogenesis / cellular response to calcium ion / positive regulation of glycolytic process / positive regulation of D-glucose import across plasma membrane / cellular response to starvation / protein localization to plasma membrane / response to activity / response to gamma radiation / regulation of microtubule cytoskeleton organization / neuron cellular homeostasis / cellular response to glucose stimulus / response to hydrogen peroxide / ADP binding / cellular response to xenobiotic stimulus / regulation of circadian rhythm / glucose metabolic process / response to estrogen / autophagy / Wnt signaling pathway / cellular response to hydrogen peroxide / kinase binding / positive regulation of T cell activation / fatty acid biosynthetic process / rhythmic process / glucose homeostasis / positive regulation of cold-induced thermogenesis / cellular response to prostaglandin E stimulus / cellular response to oxidative stress / cellular response to hypoxia / protein phosphorylation / protein kinase activity / non-specific serine/threonine protein kinase / apical plasma membrane / nuclear speck / negative regulation of translation / response to xenobiotic stimulus
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 / Immunoglobulins / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-85V / ADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / 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 / 5'-AMP-activated protein kinase catalytic subunit alpha-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.45 Å
AuthorsCalabrese, M.F. / Kurumbail, R.G.
CitationJournal: Cell Metab. / Year: 2017
Title: Activation of Skeletal Muscle AMPK Promotes Glucose Disposal and Glucose Lowering in Non-human Primates and Mice.
Authors: Cokorinos, E.C. / Delmore, J. / Reyes, A.R. / Albuquerque, B. / Kjbsted, R. / Jrgensen, N.O. / Tran, J.L. / Jatkar, A. / Cialdea, K. / Esquejo, R.M. / Meissen, J. / Calabrese, M.F. / Cordes, ...Authors: Cokorinos, E.C. / Delmore, J. / Reyes, A.R. / Albuquerque, B. / Kjbsted, R. / Jrgensen, N.O. / Tran, J.L. / Jatkar, A. / Cialdea, K. / Esquejo, R.M. / Meissen, J. / Calabrese, M.F. / Cordes, J. / Moccia, R. / Tess, D. / Salatto, C.T. / Coskran, T.M. / Opsahl, A.C. / Flynn, D. / Blatnik, M. / Li, W. / Kindt, E. / Foretz, M. / Viollet, B. / Ward, J. / Kurumbail, R.G. / Kalgutkar, A.S. / Wojtaszewski, J.F.P. / Cameron, K.O. / Miller, R.A.
History
DepositionJan 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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 / _pdbx_entry_details.has_protein_modification

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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)120,58813
Polymers118,2593
Non-polymers2,33010
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12020 Å2
ΔGint-130 kcal/mol
Surface area35850 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)241,17626
Polymers236,5176
Non-polymers4,65920
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area27290 Å2
ΔGint-271 kcal/mol
Surface area68460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.264, 124.264, 401.569
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. exp.) Mus musculus (house mouse)
Gene: Prkaa1, Ampk1, Prkaa1 / Production host: Escherichia coli (E. coli)
References: UniProt: P54645, UniProt: Q5EG47, non-specific serine/threonine 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: 23045.273 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, 10 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-85V / 1,4:3,6-dianhydro-2-O-(6-chloro-5-{4-[1-(hydroxymethyl)cyclopropyl]phenyl}-1H-benzimidazol-2-yl)-D-mannitol


Mass: 442.892 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H23ClN2O5
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#9: 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

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Details

Has protein modificationY
Sequence detailsENGINEERED INSERTION ASGGPGGS

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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: 3.79 Å3/Da / Density % sol: 67.52 %
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: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.45→47.43 Å / Num. obs: 25121 / % possible obs: 99.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 91.98 Å2 / Rpim(I) all: 0.095 / Net I/σ(I): 9.9
Reflection shellResolution: 3.45→3.51 Å / CC1/2: 0.817 / Rpim(I) all: 35.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
BUSTER2.11.7refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.45→47.43 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.875 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 2.086 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.403 / SU Rfree Cruickshank DPI: 0.404
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1242 4.94 %RANDOM
Rwork0.193 ---
obs0.195 25121 99.9 %-
Displacement parametersBiso max: 212.29 Å2 / Biso mean: 90.7 Å2 / Biso min: 35.61 Å2
Baniso -1Baniso -2Baniso -3
1--9.1869 Å20 Å20 Å2
2---9.1869 Å20 Å2
3---18.3737 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 3.45→47.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5973 0 152 0 6125
Biso mean--115.6 --
Num. residues----817
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1929SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes102HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1047HARMONIC5
X-RAY DIFFRACTIONt_it6278HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion884SEMIHARMONIC5
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_contact7210SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6278HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg8634HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion2.42
X-RAY DIFFRACTIONt_other_torsion20.95
LS refinement shellResolution: 3.45→3.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.284 115 4.21 %
Rwork0.215 2617 -
all0.217 2732 -
obs--99.53 %
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)
10.11760.1085-0.1290.91070.74381.91310.07270.00580.0542-0.061-0.09740.1382-0.5063-0.18990.02480.17650.0512-0.022-0.022-0.1207-0.1143-32.01431.5377-16.276
21.4578-0.2718-1.3623-0.01060.84422.7153-0.01160.04130.2255-0.10840.0780.1547-0.5154-0.1536-0.06640.17440.110.011-0.0736-0.1038-0.1064-26.478239.8166-31.8294
33.1379-2.5261-0.834.29592.46953.8746-0.1376-0.81260.625-0.13560.8985-0.9516-0.29911.0079-0.7609-0.27980.12340.09960.1241-0.3796-0.0548-39.070166.655516.7461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A9 - 548
2X-RAY DIFFRACTION2{ B|* }B77 - 270
3X-RAY DIFFRACTION3{ C|* }C26 - 322

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