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

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Basic information

Entry
Database: PDB / ID: 4eaj
TitleCo-crystal of AMPK core with AMP soaked with ATP
Components
  • (5'-AMP-activated protein kinase subunit ...) x 2
  • 5'-AMP-activated protein kinase catalytic subunit alpha-1
KeywordsTRANSFERASE / AMPK
Function / homology
Function and homology information


eukaryotic elongation factor-2 kinase activator activity / Energy dependent regulation of mTOR by LKB1-AMPK / positive regulation of mitochondrial transcription / 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 ...eukaryotic elongation factor-2 kinase activator activity / Energy dependent regulation of mTOR by LKB1-AMPK / positive regulation of mitochondrial transcription / 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 / 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 fatty acid oxidation / positive regulation of skeletal muscle tissue development / CAMKK-AMPK signaling cascade / import into nucleus / regulation of vesicle-mediated transport / 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 / positive regulation of protein targeting to mitochondrion / 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 / 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 / positive regulation of gluconeogenesis / 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 / positive regulation of glucose import / TP53 Regulates Metabolic Genes / response to gamma radiation / cellular response to glucose stimulus / response to hydrogen peroxide / regulation of circadian rhythm / ADP binding / fatty acid biosynthetic process / autophagy / 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 / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / nuclear speck / response to xenobiotic stimulus / apical plasma membrane / axon / protein phosphorylation / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body
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 / 5'-AMP-activated protein kinase beta subunit, interation domain / AMPK, C-terminal adenylate sensor 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 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / 5'-AMP-activated protein kinase subunit beta-2 / 5'-AMP-activated protein kinase catalytic subunit alpha-1 / 5'-AMP-activated protein kinase subunit gamma-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.609 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

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


Theoretical massNumber of molelcules
Total (without water)60,7806
Polymers59,4193
Non-polymers1,3623
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-37 kcal/mol
Surface area21190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.104, 116.006, 48.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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 / 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, [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-2 / AMPK subunit beta-2


Mass: 9886.648 Da / Num. of mol.: 1 / Fragment: UNP residues 189-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAB2 / Production host: Escherichia coli (E. coli) / References: UniProt: O43741
#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

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Non-polymers , 3 types, 57 molecules

#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 46.86 % / Mosaicity: 0.678 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.26
Details: MES pH 6.26, 16% IPP, 1% 1,4-butanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.99583 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99583 Å / Relative weight: 1
ReflectionRedundancy: 5.2 % / Number: 88967 / Rmerge(I) obs: 0.116 / Χ2: 1.01 / D res high: 2.6 Å / D res low: 30 Å / Num. obs: 17204 / % possible obs: 98.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.033099.910.0590.9565.2
5.597.0310010.081.0775.6
4.895.5910010.0910.9365.6
4.444.8910010.10.7945.7
4.124.4410010.0980.8725.7
3.884.1210010.0990.9255.7
3.693.8810010.1120.9295.8
3.533.6910010.1251.1495.8
3.393.5310010.1431.1335.8
3.283.3910010.1731.3045.8
3.173.2810010.2051.1225.7
3.083.1710010.2261.1565.7
33.0810010.251.0265.5
2.93310010.2751.035.3
2.862.9399.610.321.0095.1
2.82.8699.710.3351.0034.6
2.742.899.310.3930.9644.3
2.692.7496.510.3510.913.7
2.642.6991.910.3490.9413.3
2.62.6485.810.3970.8572.9
ReflectionResolution: 2.6→30 Å / Num. all: 17430 / Num. obs: 17204 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.64 Å / % possible all: 85.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V92

2v92


Resolution: 2.609→29.609 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8244 / SU ML: 0.35 / σ(F): 0.08 / Phase error: 24.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.258 826 5.03 %random
Rwork0.2015 ---
obs0.2043 16423 94.21 %-
all-17430 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.543 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso max: 156.75 Å2 / Biso mean: 48.9522 Å2 / Biso min: 14.51 Å2
Baniso -1Baniso -2Baniso -3
1-5.7078 Å20 Å2-0 Å2
2---1.0958 Å20 Å2
3----4.6121 Å2
Refinement stepCycle: LAST / Resolution: 2.609→29.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3544 0 85 54 3683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053710
X-RAY DIFFRACTIONf_angle_d1.0325045
X-RAY DIFFRACTIONf_chiral_restr0.06591
X-RAY DIFFRACTIONf_plane_restr0.004604
X-RAY DIFFRACTIONf_dihedral_angle_d19.9571349
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 (%)
2.6094-2.77280.30131300.23882156228681
2.7728-2.98670.27871440.22412472261692
2.9867-3.28690.30681210.21922647276896
3.2869-3.76170.25151470.19382682282998
3.7617-4.73620.22661380.16372751288999
4.7362-29.61060.24091460.20432889303599
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)
10.18460.1709-0.18471.0215-0.7870.3190.1682-0.12580.09050.4877-0.1605-0.121-0.22920.0999-00.3575-0.0881-0.18030.2586-0.05370.42043.94339.4771-13.7987
20.15960.20850.13590.230.26850.304-0.04950.21030.31760.0562-0.2308-0.99360.14940.1475-00.2910.00260.0410.43350.08030.685710.715829.0297-18.8639
30.57740.5081-0.47690.3306-0.16221.0967-0.14420.3915-0.0852-0.1705-0.11590.3544-0.14640.1419-00.29770.0197-0.06370.2366-0.01790.40890.445836.6045-21.2222
40.12780.14030.04640.13410.03290.0099-0.2629-0.04660.04210.46270.497-0.7557-0.16350.641400.2790.0106-0.0920.3323-0.03540.32272.085726.8124-12.019
50.29830.0672-0.14430.0843-0.05460.1990.1251-0.09940.5586-0.4295-0.5449-0.5137-0.37890.43320.00740.46540.0011-0.27840.24570.07440.5539-3.400744.1068-27.5856
60.069-0.0679-0.00720.0657-0.04550.01840.70540.5620.882-0.40640.27430.93390.18160.2674-00.5387-0.03470.02910.36220.04650.5623-13.233734.9134-23.0428
70.1310.04630.09460.2148-0.11170.1051-0.0023-0.17080.5654-0.04230.1704-0.03-0.00720.18500.2626-0.0690.04890.2939-0.0710.2553-7.291830.7039-19.4036
80.0238-0.03230.02760.0488-0.01370.02980.39930.16090.2752-0.0521-0.08090.1718-0.22190.077600.47650.09060.04830.4272-0.18260.4747-9.886330.5189-2.6683
90.24070.2945-0.20110.3589-0.12580.13950.0167-0.03930.2574-0.1255-0.0528-0.2971-0.34910.156500.25-0.0118-0.0170.2422-0.03230.1984-7.04921.2012-19.7473
100.4739-0.0406-0.06660.6155-0.42731.28740.0325-0.0077-0.02590.0738-0.0255-0.133-0.2273-0.0772-00.12610.0443-0.02360.1708-0.03170.164-12.66310.94-8.3677
110.17840.1533-0.07650.15050.01230.0186-0.0853-0.61060.0879-0.7245-0.29270.3098-0.3830.8008-00.558-0.09910.0450.61740.04850.2328-8.676911.99475.0542
122.03540.99540.12521.40180.19340.9517-0.04240.0358-0.1029-0.08910.0289-0.11920.2667-0.055100.18770.0384-0.03940.1319-0.00740.119-18.33-1.4163-16.7417
130.11220.371-0.09180.43470.14470.5869-0.0037-0.2785-0.03690.3381-0.23540.1311-0.0801-0.3489-00.3305-0.0256-0.02060.3424-0.10520.2579-32.64915.337-2.9323
140.0644-0.06380.08480.025-0.02650.03320.42520.37410.50140.0410.359-0.47030.0607-0.570801.34880.0299-0.1740.6683-0.03660.9235-36.654112.5014-12.2365
150.37110.0673-0.34590.67950.3010.37710.15640.0925-0.01980.0111-0.1774-0.02-0.0015-0.29400.2343-0.0507-0.00580.2491-0.02280.2098-30.4124-5.9549-18.2541
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 394:425)A394 - 425
2X-RAY DIFFRACTION2(chain A and resid 426:445)A426 - 445
3X-RAY DIFFRACTION3(chain A and resid 446:472)A446 - 472
4X-RAY DIFFRACTION4(chain A and resid 473:493)A473 - 493
5X-RAY DIFFRACTION5(chain B and resid 204:210)B204 - 210
6X-RAY DIFFRACTION6(chain B and resid 211:236)B211 - 236
7X-RAY DIFFRACTION7(chain B and resid 237:245)B237 - 245
8X-RAY DIFFRACTION8(chain B and resid 246:251)B246 - 251
9X-RAY DIFFRACTION9(chain B and resid 252:271)B252 - 271
10X-RAY DIFFRACTION10(chain C and resid 26:106)C26 - 106
11X-RAY DIFFRACTION11(chain C and resid 107:126)C107 - 126
12X-RAY DIFFRACTION12(chain C and resid 127:222)C127 - 222
13X-RAY DIFFRACTION13(chain C and resid 223:265)C223 - 265
14X-RAY DIFFRACTION14(chain C and resid 266:273)C266 - 273
15X-RAY DIFFRACTION15(chain C and resid 274:324)C274 - 324

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