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- PDB-4rew: Crystal structure of the non-phosphorylated human alpha1 beta2 ga... -

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Basic information

Entry
Database: PDB / ID: 4rew
TitleCrystal structure of the non-phosphorylated human alpha1 beta2 gamma1 holo-AMPK complex
Components
  • 5'-AMP-activated protein kinase catalytic subunit alpha-1
  • 5'-AMP-activated protein kinase subunit beta-2
  • 5'-AMP-activated protein kinase subunit gamma-1
KeywordsTRANSFERASE / human alpha1 beta2 gamma1 holo-AMPK complex / serine/threonine protein kinase / Axin / CaMKKbeta / LKB1 / glycogen / phosphorylation
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 / AMPK inhibits chREBP transcriptional activation activity / regulation of peptidyl-serine phosphorylation / cold acclimation ...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 / AMPK inhibits chREBP transcriptional activation activity / regulation of peptidyl-serine phosphorylation / cold acclimation / positive regulation of peptidyl-lysine acetylation / lipid droplet disassembly / Lipophagy / regulation of bile acid secretion / positive regulation of skeletal muscle tissue development / CAMKK-AMPK signaling cascade / import into nucleus / cAMP-dependent protein kinase regulator activity / regulation of vesicle-mediated transport / positive regulation of cholesterol biosynthetic process / cellular response to organonitrogen compound / nucleotide-activated protein kinase complex / Energy dependent regulation of mTOR by LKB1-AMPK / Carnitine metabolism / negative regulation of hepatocyte apoptotic process / tau-protein kinase / bile acid and bile salt transport / protein kinase regulator activity / cellular response to ethanol / protein localization to lipid droplet / negative regulation of TOR signaling / bile acid signaling pathway / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / response to caffeine / motor behavior / regulation of glycolytic process / positive regulation of protein targeting to mitochondrion / cAMP-dependent protein kinase activity / lipid biosynthetic process / negative regulation of tubulin deacetylation / AMP-activated protein kinase activity / Macroautophagy / positive regulation of protein localization / tau-protein kinase activity / AMP binding / cholesterol biosynthetic process / fatty acid oxidation / cellular response to nutrient levels / positive regulation of protein kinase activity / fatty acid homeostasis / negative regulation of lipid catabolic process / cellular response to glucose starvation / positive regulation of autophagy / energy homeostasis / Activation of AMPK downstream of NMDARs / regulation of microtubule cytoskeleton organization / response to UV / negative regulation of TORC1 signaling / positive regulation of adipose tissue development / cellular response to calcium ion / negative regulation of insulin receptor signaling pathway / positive regulation of glycolytic process / response to activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / response to gamma radiation / cellular response to glucose stimulus / tau protein binding / ADP binding / regulation of circadian rhythm / autophagy / fatty acid biosynthetic process / Wnt signaling pathway / cellular response to hydrogen peroxide / neuron cellular homeostasis / response to estrogen / cellular response to prostaglandin E stimulus / glucose metabolic process / rhythmic process / cellular response to xenobiotic stimulus / glucose homeostasis / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / cellular response to hypoxia / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / response to hypoxia / protein kinase activity / nuclear speck / apical plasma membrane / axon / protein phosphorylation / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / chromatin binding / dendrite / chromatin
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 / STAUROSPORINE / 5'-AMP-activated protein kinase subunit beta-2 / 5'-AMP-activated protein kinase subunit gamma-1 / 5'-AMP-activated protein kinase catalytic subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.58 Å
AuthorsZhou, X.E. / Ke, J. / Li, X. / Wang, L. / Gu, X. / de Waal, P.W. / Tan, M.H.E. / Wang, D. / Wu, D. / Xu, H.E. / Melcher, K.
CitationJournal: Cell Res. / Year: 2015
Title: Structural basis of AMPK regulation by adenine nucleotides and glycogen.
Authors: Li, X. / Wang, L. / Zhou, X.E. / Ke, J. / de Waal, P.W. / Gu, X. / Tan, M.H. / Wang, D. / Wu, D. / Xu, H.E. / Melcher, K.
History
DepositionSep 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Mar 11, 2015Group: Structure summary
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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-2
G: 5'-AMP-activated protein kinase subunit gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,0097
Polymers118,5013
Non-polymers1,5084
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14120 Å2
ΔGint-70 kcal/mol
Surface area37000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.900, 126.900, 188.794
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Detailshuman alpha1 beta2 gamma1 heterotrimeric complex

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Components

#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: 61486.152 Da / Num. of mol.: 1 / Fragment: Human AMPK alpha1 subunit [G11-Q550] / Mutation: E471G, E474A, K476A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMPK1, human holo-AMPK alpha1 subunit, PRKAA1 / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q13131, non-specific serine/threonine protein kinase, [acetyl-CoA carboxylase] kinase, [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase, tau-protein kinase
#2: Protein 5'-AMP-activated protein kinase subunit beta-2 / AMPK subunit beta-2


Mass: 22369.527 Da / Num. of mol.: 1 / Fragment: Human AMPK beta2 subunit [A76-I272]
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: human holo-AMPK beta2 subunit, PRKAB2 / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O43741
#3: Protein 5'-AMP-activated protein kinase subunit gamma-1 / AMPK gamma1 / AMPK subunit gamma-1 / AMPKg


Mass: 34645.109 Da / Num. of mol.: 1 / Fragment: Human AMPK gamma1 subunit [S24-G327]
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: human holo-AMPK gamma1 subunit, PRKAG1 / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P54619
#4: 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
#5: 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: 3.7 Å3/Da / Density % sol: 66.78 %
Crystal growTemperature: 293 K / pH: 6.8
Details: 0.1 M N-acetamido-iminodiacetic acid, pH 6.8, 9% 2-methyl-2,4-pentanediol, and 11.5 mM C-HEGA, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 2, 2012
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 4.6→30 Å / Num. obs: 10287 / % possible obs: 100 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 20
Reflection shellResolution: 4.6→4.68 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y94

2y94
PDB Unreleased entry


Resolution: 4.58→29.01 Å / SU ML: 0.48 / σ(F): 1.35 / Phase error: 31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.259 729 7.11 %
Rwork0.232 --
obs0.234 10260 99.7 %
all-10294 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.58→29.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6395 0 104 0 6499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046661
X-RAY DIFFRACTIONf_angle_d0.9169040
X-RAY DIFFRACTIONf_dihedral_angle_d18.6652518
X-RAY DIFFRACTIONf_chiral_restr0.0361014
X-RAY DIFFRACTIONf_plane_restr0.0051116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.5778-4.92960.30261150.29261865X-RAY DIFFRACTION99
4.9296-5.42280.32581400.29551893X-RAY DIFFRACTION100
5.4228-6.20080.29561280.29071898X-RAY DIFFRACTION100
6.2008-7.78730.31571670.27521903X-RAY DIFFRACTION100
7.7873-29.00630.21291790.17691972X-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)
11.2236-0.56060.73215.0648-0.47622.06170.0583-0.0897-0.20240.20940.02330.2173-0.075-0.155502.1447-0.01730.06052.4726-0.00952.266661.9453-38.644515.3947
21.1963-0.60930.21681.89421.61691.8562-0.0894-0.2179-0.3628-0.044-0.2602-0.23430.0362-0.096702.2311-0.18310.04482.6010.11532.186258.2119-23.32748.6703
32.32020.58630.43234.207-0.85446.32260.0171-0.1845-0.0707-0.15310.00180.6670.1254-0.6073-01.80170.0832-0.16042.0233-0.08572.211339.3176-19.1732-16.3325
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain G

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