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- PDB-6c9f: AMP-activated protein kinase bound to pharmacological activator R734 -

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Basic information

Entry
Database: PDB / ID: 6c9f
TitleAMP-activated protein kinase bound to pharmacological activator R734
Components
  • (5'-AMP-activated protein kinase subunit ...) x 2
  • 5'-AMP-activated protein kinase catalytic subunit alpha-1,5'-AMP-activated protein kinase catalytic subunit alpha-1
KeywordsTRANSFERASE / AMPK / activator
Function / homology
Function and homology information


negative regulation of glucosylceramide biosynthetic process / positive regulation of mitochondrial transcription / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / : / regulation of stress granule assembly / histone H2BS36 kinase activity / regulation of peptidyl-serine phosphorylation / cold acclimation ...negative regulation of glucosylceramide biosynthetic process / positive regulation of mitochondrial transcription / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / : / regulation of stress granule assembly / histone H2BS36 kinase activity / regulation of peptidyl-serine phosphorylation / cold acclimation / positive regulation of peptidyl-lysine acetylation / lipid droplet disassembly / Lipophagy / regulation of bile acid secretion / import into nucleus / positive regulation of skeletal muscle tissue development / CAMKK-AMPK signaling cascade / cAMP-dependent protein kinase regulator activity / regulation of vesicle-mediated transport / positive regulation of cholesterol biosynthetic process / cellular response to organonitrogen compound / protein kinase regulator activity / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of TOR signaling / negative regulation of hepatocyte apoptotic process / tau-protein kinase / bile acid and bile salt transport / nucleotide-activated protein kinase complex / cellular response to ethanol / protein localization to lipid droplet / bile acid signaling pathway / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / response to caffeine / motor behavior / positive regulation of protein targeting to mitochondrion / lipid biosynthetic process / regulation of glycolytic process / cAMP-dependent protein kinase activity / negative regulation of tubulin deacetylation / Macroautophagy / AMP-activated protein kinase activity / positive regulation of protein localization / tau-protein kinase activity / cholesterol biosynthetic process / AMP binding / fatty acid oxidation / cellular response to nutrient levels / fatty acid homeostasis / positive regulation of protein kinase activity / cellular response to glucose starvation / Activation of AMPK downstream of NMDARs / negative regulation of lipid catabolic process / regulation of microtubule cytoskeleton organization / positive regulation of autophagy / energy homeostasis / response to UV / negative regulation of insulin receptor signaling pathway / negative regulation of TORC1 signaling / positive regulation of adipose tissue development / cellular response to calcium ion / positive regulation of glycolytic process / response to activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / ADP binding / cellular response to glucose stimulus / response to gamma radiation / TP53 Regulates Metabolic Genes / tau protein binding / regulation of circadian rhythm / cellular response to hydrogen peroxide / Wnt signaling pathway / autophagy / neuron cellular homeostasis / cellular response to prostaglandin E stimulus / response to estrogen / fatty acid biosynthetic process / glucose metabolic process / rhythmic process / cellular response to xenobiotic stimulus / glucose homeostasis / cellular response to oxidative stress / positive regulation of cold-induced thermogenesis / cellular response to hypoxia / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / nuclear speck / apical plasma membrane / axon / negative regulation of gene expression / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / neuronal cell body / chromatin binding / positive regulation of cell population proliferation
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 / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase ...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 / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / 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 / 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
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Chem-R34 / STAUROSPORINE / 5'-AMP-activated protein kinase subunit gamma-1 / 5'-AMP-activated protein kinase catalytic subunit alpha-1 / 5'-AMP-activated protein kinase subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.924 Å
AuthorsYan, Y. / Zhou, X.E. / Novick, S. / Shaw, S.J. / Li, Y. / Hitoshi, Y. / Brunzelle, J.S. / Griffin, P.R. / Xu, H.E. / Melcher, K.
Funding support United States, China, 9items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102545 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK071662 United States
National Natural Science Foundation of China (NSFC)31300245 China
Ministry of Science and Technology (MoST, China)2012ZX09301001 China
Ministry of Science and Technology (MoST, China)2012CB910403 China
Ministry of Science and Technology (MoST, China)2013CB910600 China
Ministry of Science and Technology (MoST, China)XDB08020303 China
Ministry of Science and Technology (MoST, China)2013ZX09507001 China
Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor085P1000817 United States
CitationJournal: J. Biol. Chem. / Year: 2019
Title: Structures of AMP-activated protein kinase bound to novel pharmacological activators in phosphorylated, non-phosphorylated, and nucleotide-free states.
Authors: Yan, Y. / Zhou, X.E. / Novick, S.J. / Shaw, S.J. / Li, Y. / Brunzelle, J.S. / Hitoshi, Y. / Griffin, P.R. / Xu, H.E. / Melcher, K.
History
DepositionJan 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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-1,5'-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)119,8988
Polymers117,9433
Non-polymers1,9555
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12960 Å2
ΔGint-66 kcal/mol
Surface area40150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.289, 123.289, 406.594
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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-1,5'-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: 57245.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAA1, AMPK1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13131, non-specific serine/threonine protein kinase, [acetyl-CoA carboxylase] kinase, [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


Mass: 23071.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAB1, AMPK / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y478
#3: Protein 5'-AMP-activated protein kinase subunit gamma-1 / AMPKg


Mass: 37626.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAG1 / Production host: Escherichia coli (E. coli) / References: UniProt: P54619

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Non-polymers , 3 types, 5 molecules

#4: Chemical ChemComp-R34 / 5-{[6-chloro-5-(1-methyl-1H-indol-5-yl)-1H-benzimidazol-2-yl]oxy}-N-hydroxy-2-methylbenzamide


Mass: 446.886 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H19ClN4O3
#5: Chemical ChemComp-STU / STAUROSPORINE / Staurosporine


Mass: 466.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM
#6: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*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: 3.78 Å3/Da / Density % sol: 67.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M tri-sodium acetate pH 5.6, 0.2 M ammonium acetate, 15% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.92→50 Å / Num. obs: 40620 / % possible obs: 99.9 % / Redundancy: 8.8 % / Net I/σ(I): 14.5
Reflection shellResolution: 2.92→3.06 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.924→49.671 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2449 2918 7.18 %
Rwork0.2279 --
obs0.2292 40620 99.92 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.924→49.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6855 0 136 0 6991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037169
X-RAY DIFFRACTIONf_angle_d0.7199745
X-RAY DIFFRACTIONf_dihedral_angle_d11.5122650
X-RAY DIFFRACTIONf_chiral_restr0.0271097
X-RAY DIFFRACTIONf_plane_restr0.0041203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.924-3.02850.34162480.32623705X-RAY DIFFRACTION100
3.0285-3.14970.35093000.30723684X-RAY DIFFRACTION100
3.1497-3.2930.29332880.28483681X-RAY DIFFRACTION100
3.293-3.46660.28422670.253717X-RAY DIFFRACTION100
3.4666-3.68370.2352780.23843732X-RAY DIFFRACTION100
3.6837-3.96810.23512810.22373746X-RAY DIFFRACTION100
3.9681-4.36720.2332960.1993739X-RAY DIFFRACTION100
4.3672-4.99860.20223000.1913795X-RAY DIFFRACTION100
4.9986-6.29570.22283000.21113844X-RAY DIFFRACTION100
6.2957-49.67840.22773600.20574059X-RAY DIFFRACTION100
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)
10.003-0.0018-0.00610.03380.02490.0314-0.10150.0274-0.06310.0078-0.0679-0.0738-0.0332-0.0275-0.03470.28680.0149-0.05720.1108-0.17920.1297-25.81725.0722-16.7153
20.0058-0.03380.0022-0.0086-0.0076-0.0078-0.00280.04310.0357-0.0325-0.06170.0988-0.0699-0.0657-00.72210.27250.02280.5978-0.20760.5504-50.525250.3416-15.1161
30.0161-0.0021-0.00040.00290.00010.0048-0.01250.0197-0.010.0264-0.0258-0.014-0.0236-0.01320.00070.3027-0.1039-0.04630.2903-0.09170.2572-11.957734.0723-51.6784
40.0139-0.0014-0.0126-0.00030.00810.00030.0216-0.0560.00490.04620.01270.0559-0.0113-0.021900.67470.18850.0840.7034-0.17290.5887-43.840847.8702-8.9243
50.0012-0.0014-0.00110.00060.0014-0.0004-0.0118-0.0019-0.00620.0088-0.0082-0-0.00660.0138-00.4910.01020.11730.5686-0.0250.5699-24.247959.84365.8987
60.0027-0.0002-0.00220.00290.00040.0004-0.0056-0.0120.0028-0.0137-0.0111-0.0096-0.00750.0031-00.5290.1410.17370.4365-0.1490.5287-49.984866.4247.2233
70.0005-0.0011-0.0003-000.0011-0.0040.0013-0.00160.00190.0036-0.0018-0.0023-0.002600.46690.08640.00220.4737-0.04210.5032-62.867271.15816.2275
80.00070.0011-0.00130.0007-0.0004-0.0006-0.01690.00010.0029-0.0113-0.0079-0.0113-0.0076-0.002600.6411-0.0020.08780.6156-0.03580.6156-43.195974.63094.0765
90.0004-0.0006-0.0012-0.00040.00150.00090.0073-0.0236-0.00910.0176-0.0077-0.0228-0.00130.0158-00.7262-0.00020.19370.7559-0.09960.7809-29.111563.42937.8633
100.0046-0.0010.0003-0.0030.0116-0.00170.0076-0.00010.01370.02160.014-0.0213-0.02620.0047-00.3220.06310.08890.4359-0.17560.5246-36.273469.071128.3926
110.00070.0006-0.0006-0.0003-0.00010.00020.0059-0.0031-0.01980.00730.0003-0.01020.011-0.0084-00.53780.0550.06060.5908-0.0060.6224-52.79760.156728.1087
120.0021-0.0020.00020.00110.0011-0.00020.00910.0083-0.0190.00470.0132-0.0026-0.00330.004400.64790.00840.06270.7523-0.15020.9082-27.524864.228.3144
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 276 )
2X-RAY DIFFRACTION2chain 'A' and (resid 277 through 549 )
3X-RAY DIFFRACTION3chain 'B' and (resid 74 through 161 )
4X-RAY DIFFRACTION4chain 'B' and (resid 162 through 270 )
5X-RAY DIFFRACTION5chain 'C' and (resid 25 through 48 )
6X-RAY DIFFRACTION6chain 'C' and (resid 49 through 97 )
7X-RAY DIFFRACTION7chain 'C' and (resid 98 through 112 )
8X-RAY DIFFRACTION8chain 'C' and (resid 113 through 136 )
9X-RAY DIFFRACTION9chain 'C' and (resid 137 through 181 )
10X-RAY DIFFRACTION10chain 'C' and (resid 182 through 250 )
11X-RAY DIFFRACTION11chain 'C' and (resid 251 through 271 )
12X-RAY DIFFRACTION12chain 'C' and (resid 272 through 324 )

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