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- PDB-4eal: Co-crystal of AMPK core with ATP soaked with AMP -

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Basic information

Entry
Database: PDB / ID: 4eal
TitleCo-crystal of AMPK core with ATP soaked with AMP
Components
  • 5'-AMP-activated protein kinase catalytic subunit alpha-1
  • 5'-AMP-activated protein kinase subunit beta-1
  • 5'-AMP-activated protein kinase subunit gamma-1
KeywordsTRANSFERASE / AMPK
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 / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / positive regulation of mitochondrial transcription ...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 / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / positive regulation of mitochondrial transcription / histone H2BS36 kinase activity / cold acclimation / AMP-activated protein kinase activity / lipid droplet disassembly / regulation of carbon utilization / positive regulation of skeletal muscle tissue development / CAMKK-AMPK signaling cascade / import into nucleus / 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 / protein kinase regulator activity / negative regulation of TOR signaling / response to caffeine / positive regulation of protein targeting to mitochondrion / regulation of glycolytic process / protein localization to lipid droplet / negative regulation of tubulin deacetylation / AMP binding / cellular response to stress / cholesterol biosynthetic process / lipid biosynthetic process / 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 / negative regulation of TORC1 signaling / positive regulation of adipose tissue development / positive regulation of autophagy / positive regulation of gluconeogenesis / negative regulation of insulin receptor signaling pathway / cellular response to calcium ion / regulation of microtubule cytoskeleton organization / positive regulation of glycolytic process / response to gamma radiation / response to activity / positive regulation of D-glucose import across plasma membrane / cellular response to glucose stimulus / response to hydrogen peroxide / neuron cellular homeostasis / ADP binding / regulation of circadian rhythm / positive regulation of T cell activation / autophagy / response to estrogen / cellular response to xenobiotic stimulus / Wnt signaling pathway / cellular response to hydrogen peroxide / glucose metabolic process / fatty acid biosynthetic process / rhythmic process / glucose homeostasis / cellular response to prostaglandin E stimulus / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / cellular response to hypoxia / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / negative regulation of translation / nuclear speck / 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 / protein kinase binding / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / protein-containing complex binding / signal transduction / protein-containing complex / ATP binding
Similarity search - Function
Kinase associated domain 1, KA1 / 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 ...Kinase associated domain 1, KA1 / 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 / TATA-Binding Protein / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / 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
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.506 Å
AuthorsChen, L. / Wang, J. / Zhang, Y.-Y. / Yan, S.F. / Neumann, D. / Schlattner, U. / Wang, Z.-X. / Wu, J.-W.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: AMP-activated protein kinase undergoes nucleotide-dependent conformational changes
Authors: Chen, L. / Wang, J. / Zhang, Y.-Y. / Yan, S.F. / Neumann, D. / Schlattner, U. / Wang, Z.-X. / Wu, J.-W.
History
DepositionMar 22, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref_seq_dif
Item: _entity.details / _entity.pdbx_description ..._entity.details / _entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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-1
C: 5'-AMP-activated protein kinase subunit gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3605
Polymers57,6663
Non-polymers6942
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-32 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.850, 40.503, 77.738
Angle α, β, γ (deg.)90.00, 105.53, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-306-

HOH

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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: 12097.888 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Chimera protein of residues 405-479 and residues 540-559 from 5'-AMP-activated protein kinase catalytic subunit alpha-1 (Uniprot P54645), linked by linker GGGGGG
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prkaa1, Ampk1 / Production host: Escherichia coli (E. coli)
References: UniProt: P54645, non-specific serine/threonine protein kinase, EC: 2.7.11.27, [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase, tau-protein kinase
#2: Protein 5'-AMP-activated protein kinase subunit beta-1 / AMPKb / 5'-AMP-activated protein kinase 40 kDa subunit


Mass: 8133.786 Da / Num. of mol.: 1 / Fragment: UNP residues 200-270
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
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 0.1M MES pH5.9, 18% IPP, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 18505 / Num. obs: 18431 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 58.77 Å2
Reflection shellResolution: 2.5→2.54 Å / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V8Q

2v8q


Resolution: 2.506→24.967 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7758 / SU ML: 0.4 / σ(F): 0.07 / Phase error: 28.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2774 884 4.97 %
Rwork0.2324 --
obs0.2347 17779 95.98 %
all-18505 -
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.154 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso max: 179.85 Å2 / Biso mean: 75.9218 Å2 / Biso min: 28.08 Å2
Baniso -1Baniso -2Baniso -3
1--1.8684 Å20 Å2-9.1271 Å2
2--1.1113 Å2-0 Å2
3---0.7571 Å2
Refinement stepCycle: LAST / Resolution: 2.506→24.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3389 0 46 58 3493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033505
X-RAY DIFFRACTIONf_angle_d0.7294754
X-RAY DIFFRACTIONf_chiral_restr0.046566
X-RAY DIFFRACTIONf_plane_restr0.002575
X-RAY DIFFRACTIONf_dihedral_angle_d16.5381280
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5061-2.66290.29971290.27232569269889
2.6629-2.86820.31751370.26472721285894
2.8682-3.15640.28611270.25372836296397
3.1564-3.61190.30771700.23832874304499
3.6119-4.54620.21941650.19972932309799
4.5462-24.9680.27761560.21882963311998
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)
11.2752-0.135-0.89250.8817-0.13421.256-0.33330.6355-0.7548-0.051-0.49020.2804-0.10531.15660.70690.4418-0.0252-0.23071.04720.31520.961426.3452394.3026-22.876
20.3168-0.03720.13560.0066-0.02520.0512-0.0179-0.2916-0.0066-0.13220.2242-0.0719-0.08740.2357-0.03020.6855-0.0294-0.27682.30581.03190.969340.8558399.6048-15.467
33.22260.45-1.53740.1616-0.14530.76030.1924-1.04781.3754-0.22380.2851-0.1134-0.11520.4884-0.10840.5251-0.2047-0.3731.5570.55771.270433.4782404.1052-11.2575
40.95760.8501-1.51112.3617-0.76512.82190.279-1.1524-0.0344-0.0328-0.42040.5463-0.42792.07980.09890.8852-0.3104-0.35791.6750.23980.995629.641401.7625-4.6297
52.38381.1413-1.3131.8289-1.24472.79410.5967-1.23810.06040.1731-0.548-0.044-0.40291.1325-0.07040.7738-0.1516-0.08941.1485-0.10990.691417.5158404.8183-2.2409
61.32880.36620.79960.9037-0.38742.46650.4353-0.8214-0.16910.5806-0.6414-0.2674-0.4977-0.54750.09320.5523-0.2734-0.18721.31380.46480.47925.7087395.1745-8.5839
70.8674-0.42620.66432.0818-1.09490.82850.52840.0705-0.28480.0605-1.5912-1.19240.37431.46771.00860.57740.06640.12121.41380.64990.830335.7616391.6132-21.0745
81.28141.9953-1.06713.0057-1.92652.06420.31-1.0398-0.20.6167-0.8822-0.8145-0.2271.04660.51420.3779-0.1246-0.13460.58670.16910.568919.2893400.9454-12.5462
90.0898-0.1697-0.02250.8154-0.83051.3024-0.39540.1214-0.2952-0.9248-1.4820.64770.6310.53550.63091.33850.59790.51221.1631.1180.736527.4021385.3287-13.9294
103.44440.11780.24030.93021.27671.7860.64050.4474-0.4842-0.62310.3854-0.0310.0470.1339-0.73420.69890.0275-0.05940.47850.16470.499918.1441395.7566-21.7937
110.68560.7590.03972.1772-1.67661.25510.0867-0.0093-0.0630.4446-0.3819-0.2792-0.47210.0580.12130.43640.14580.02210.41880.05350.307310.5421394.7141-16.745
120.6279-0.18020.2520.7244-0.95680.4863-0.0202-0.1031-0.0894-0.0197-0.1475-0.1437-0.1423-0.16870.12460.43010.07680.02940.2823-0.11590.2242-3.6642393.2004-18.4279
130.4309-0.1866-0.1587-0.0378-0.26490.23290.1307-0.06730.2111-0.2863-0.06460.2039-0.2657-0.02-0.02670.52560.0508-0.04490.2382-0.10740.3153-1.1739408.4439-22.1685
141.2574-0.0930.05371.04910.15431.52020.1012-0.25120.25550.2019-0.18360.0597-0.2219-0.10760.04030.33070.1060.03270.2712-0.1180.2794-6.5931399.9839-16.0998
150.40860.55340.93052.2634-1.39582.91090.2141-0.390.19220.29660.36460.8834-0.0225-1.516-0.24480.3915-0.0548-0.0980.9934-0.0690.5289-27.8748389.0327-24.0179
161.20130.4867-0.27491.4972-0.241.0166-0.12240.542-0.1103-0.00590.1036-0.1461-0.391-0.5297-0.00840.47150.2312-0.03060.6182-0.14760.4525-16.1058404.841-38.3903
170.96341.4686-1.44491.144-0.78212.7078-0.090.5783-0.6013-0.1544-0.0556-0.43270.0395-0.79490.06240.33320.0318-0.10310.6641-0.05040.6089-18.2448395.5077-38.7672
180.39260.0903-0.38430.5064-0.26670.803-0.16070.49990.2978-0.08270.1310.02070.0998-0.71330.01810.231-0.0059-0.04720.5543-0.12610.5101-22.8112390.8084-28.1721
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 396:403)A396 - 403
2X-RAY DIFFRACTION2(chain A and resid 404:408)A404 - 408
3X-RAY DIFFRACTION3(chain A and resid 409:417)A409 - 417
4X-RAY DIFFRACTION4(chain A and resid 418:431)A418 - 431
5X-RAY DIFFRACTION5(chain A and resid 432:443)A432 - 443
6X-RAY DIFFRACTION6(chain A and resid 444:453)A444 - 453
7X-RAY DIFFRACTION7(chain A and resid 454:461)A454 - 461
8X-RAY DIFFRACTION8(chain A and resid 462:548)A462 - 548
9X-RAY DIFFRACTION9(chain B and resid 202:235)B202 - 235
10X-RAY DIFFRACTION10(chain B and resid 236:246)B236 - 246
11X-RAY DIFFRACTION11(chain B and resid 247:270)B247 - 270
12X-RAY DIFFRACTION12(chain C and resid 23:68)C23 - 68
13X-RAY DIFFRACTION13(chain C and resid 69:107)C69 - 107
14X-RAY DIFFRACTION14(chain C and resid 108:179)C108 - 179
15X-RAY DIFFRACTION15(chain C and resid 180:207)C180 - 207
16X-RAY DIFFRACTION16(chain C and resid 208:252)C208 - 252
17X-RAY DIFFRACTION17(chain C and resid 253:287)C253 - 287
18X-RAY DIFFRACTION18(chain C and resid 288:324)C288 - 324

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