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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 / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / histone H2BS36 kinase activity / cold acclimation / AMP-activated protein kinase activity / lipid droplet disassembly / Lipophagy ...negative regulation of glucosylceramide biosynthetic process / positive regulation of mitochondrial transcription / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / histone H2BS36 kinase activity / cold acclimation / AMP-activated protein kinase activity / lipid droplet disassembly / Lipophagy / CAMKK-AMPK signaling cascade / protein localization to lipid droplet / cAMP-dependent protein kinase regulator activity / negative regulation of hepatocyte apoptotic process / regulation of vesicle-mediated transport / Energy dependent regulation of mTOR by LKB1-AMPK / 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 / motor behavior / negative regulation of TOR signaling / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / neuron cellular homeostasis / protein localization to membrane / cholesterol biosynthetic process / regulation of glycolytic process / cAMP-dependent protein kinase activity / : / response to caffeine / cellular response to stress / tau-protein kinase activity / lipid biosynthetic process / AMP binding / energy homeostasis / Macroautophagy / response to UV / negative regulation of ferroptosis / fatty acid homeostasis / cellular response to ethanol / negative regulation of lipid catabolic process / cellular response to glucose starvation / positive regulation of gluconeogenesis / cellular response to nutrient levels / Activation of AMPK downstream of NMDARs / positive regulation of protein localization / positive regulation of adipose tissue development / negative regulation of insulin receptor signaling pathway / negative regulation of TORC1 signaling / response to gamma radiation / cellular response to calcium ion / positive regulation of glycolytic process / positive regulation of autophagy / protein localization to plasma membrane / response to activity / cellular response to starvation / cellular response to xenobiotic stimulus / TP53 Regulates Metabolic Genes / cellular response to glucose stimulus / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of microtubule cytoskeleton organization / Wnt signaling pathway / positive regulation of cholesterol biosynthetic process / ADP binding / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / response to estrogen / cellular response to hydrogen peroxide / regulation of circadian rhythm / tau protein binding / positive regulation of T cell activation / autophagy / fatty acid biosynthetic process / glucose homeostasis / rhythmic process / positive regulation of cold-induced thermogenesis / ciliary basal body / cellular response to oxidative stress / spermatogenesis / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / regulation of cell cycle / protein kinase activity / protein phosphorylation / non-specific serine/threonine protein kinase / nuclear speck / apical plasma membrane / endoplasmic reticulum lumen / negative regulation of gene expression / protein serine kinase activity / axon / protein serine/threonine kinase activity / neuronal cell body / positive regulation of cell population proliferation / chromatin binding / negative regulation of apoptotic process / dendrite / protein kinase binding / positive regulation of DNA-templated transcription
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 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
Revision 1.6Oct 16, 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-1,5'-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
Water00
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, 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


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


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


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM

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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: 3.78 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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