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- PDB-4f2l: Structure of a regulatory domain of AMPK -

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Basic information

Entry
Database: PDB / ID: 4f2l
TitleStructure of a regulatory domain of AMPK
Components5'-AMP-activated protein kinase catalytic subunit alpha-1
KeywordsTRANSFERASE / regulatory domain / helix / AMPK intramolecular interaction
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 / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / positive regulation of mitochondrial transcription / cold acclimation ...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 / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / positive regulation of mitochondrial transcription / cold acclimation / lipid droplet disassembly / positive regulation of skeletal muscle tissue development / CAMKK-AMPK signaling cascade / regulation of vesicle-mediated transport / nucleotide-activated protein kinase complex / 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 / negative regulation of TOR signaling / response to caffeine / positive regulation of protein targeting to mitochondrion / protein localization to lipid droplet / negative regulation of tubulin deacetylation / lipid biosynthetic process / cholesterol biosynthetic process / cellular response to stress / fatty acid oxidation / motor behavior / cellular response to ethanol / fatty acid homeostasis / negative regulation of lipid catabolic process / cellular response to nutrient levels / response to UV / cellular response to glucose starvation / energy homeostasis / positive regulation of protein localization / positive regulation of adipose tissue development / negative regulation of TORC1 signaling / positive regulation of autophagy / positive regulation of gluconeogenesis / negative regulation of insulin receptor signaling pathway / regulation of microtubule cytoskeleton organization / cellular response to calcium ion / positive regulation of glycolytic process / response to activity / histone H2BS36 kinase activity / response to gamma radiation / positive regulation of D-glucose import / AMP-activated protein kinase activity / cellular response to glucose stimulus / response to hydrogen peroxide / regulation of circadian rhythm / positive regulation of T cell activation / autophagy / response to estrogen / Wnt signaling pathway / neuron cellular homeostasis / cellular response to hydrogen peroxide / glucose metabolic process / fatty acid biosynthetic process / rhythmic process / cellular response to xenobiotic stimulus / cellular response to prostaglandin E stimulus / glucose homeostasis / cellular response to oxidative stress / cellular response to hypoxia / non-specific serine/threonine protein kinase / protein kinase activity / negative regulation of translation / nuclear speck / protein phosphorylation / ciliary basal body / apical plasma membrane / response to xenobiotic stimulus / axon / negative regulation of gene expression / protein serine kinase activity / neuronal cell body / protein serine/threonine kinase activity / positive regulation of cell population proliferation / dendrite / chromatin binding / positive regulation of gene expression / negative regulation of apoptotic process / protein-containing complex binding / chromatin / positive regulation of DNA-templated transcription / protein-containing complex / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
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 / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / KA1 domain/Ssp2, C-terminal / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Serine/threonine-protein kinase, active site ...PRKAA1, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase alpha 1 catalytic subunit, C-terminal / : / AMP-activated protein kinase, alpha subunit, autoinhibitory domain / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / KA1 domain/Ssp2, C-terminal / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / 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. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
5'-AMP-activated protein kinase catalytic subunit alpha-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsXin, F.J. / Zhang, Y.Y. / Wang, J. / Wang, Z.X. / Wu, J.W.
CitationJournal: Nature / Year: 2013
Title: Conserved regulatory elements in AMPK
Authors: Chen, L. / Xin, F.J. / Wang, J. / Hu, J. / Zhang, Y.Y. / Wan, S. / Cao, L.S. / Lu, C. / Li, P. / Yan, S.F. / Neumann, D. / Schlattner, U. / Xia, B. / Wang, Z.X. / Wu, J.W.
History
DepositionMay 8, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _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:
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Assembly

Deposited unit
A: 5'-AMP-activated protein kinase catalytic subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4122
Polymers7,3881
Non-polymers241
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 5'-AMP-activated protein kinase catalytic subunit alpha-1
hetero molecules

A: 5'-AMP-activated protein kinase catalytic subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8244
Polymers14,7762
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area1810 Å2
ΔGint-29 kcal/mol
Surface area8510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)22.117, 36.258, 98.755
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein 5'-AMP-activated protein kinase catalytic subunit alpha-1 / AMPK subunit alpha-1 / Tau-protein kinase PRKAA1


Mass: 7387.910 Da / Num. of mol.: 1 / Fragment: regulatory domain, UNP RESIDUES 295-347
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prkaa1, Ampk1 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P54645, non-specific serine/threonine protein kinase, tau-protein kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
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: 2.68 Å3/Da / Density % sol: 54.1 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 0.3M Magnesium sulfate, 36% isopropanol (v/v), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 26, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 24489 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 36.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1179 / % possible all: 98.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AutoSolphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 1.5→24.372 Å / SU ML: 0.18 / σ(F): 1.9 / Phase error: 17.55 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2116 1198 4.9 %RANDOM
Rwork0.1819 ---
obs0.1833 24447 99.47 %-
all-24447 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.764 Å2 / ksol: 0.387 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.6331 Å20 Å20 Å2
2--5.9066 Å2-0 Å2
3----4.2735 Å2
Refinement stepCycle: LAST / Resolution: 1.5→24.372 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms508 0 1 79 588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005538
X-RAY DIFFRACTIONf_angle_d0.902730
X-RAY DIFFRACTIONf_dihedral_angle_d15.646207
X-RAY DIFFRACTIONf_chiral_restr0.06878
X-RAY DIFFRACTIONf_plane_restr0.00398
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5001-1.56010.2471500.2275256299
1.5601-1.63110.23321320.19872603100
1.6311-1.71710.19281630.17842559100
1.7171-1.82460.22311380.18332575100
1.8246-1.96550.2349910.16822633100
1.9655-2.16310.19851280.17962600100
2.1631-2.47590.1781470.17552595100
2.4759-3.11830.22051410.182255499
3.1183-24.37530.22271080.182256898

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