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- PDB-4eai: Co-crystal structure of an AMPK core with AMP -

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Basic information

Entry
Database: PDB / ID: 4eai
TitleCo-crystal structure of an AMPK core with AMP
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 / 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 / positive regulation of mitochondrial transcription / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / AMPK inhibits chREBP transcriptional activation activity ...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 / positive regulation of mitochondrial transcription / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / AMPK inhibits chREBP transcriptional activation activity / cold acclimation / lipid droplet disassembly / Lipophagy / 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 / positive regulation of fatty acid oxidation / Energy dependent regulation of mTOR by LKB1-AMPK / positive regulation of T cell mediated immune response to tumor cell / Carnitine shuttle / tau-protein kinase / negative regulation of hepatocyte apoptotic process / cellular response to ethanol / protein kinase regulator activity / negative regulation of TOR signaling / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / response to caffeine / positive regulation of protein targeting to mitochondrion / regulation of glycolytic process / protein localization to lipid droplet / motor behavior / lipid biosynthetic process / negative regulation of tubulin deacetylation / Macroautophagy / cellular response to stress / cholesterol biosynthetic process / AMP binding / fatty acid oxidation / fatty acid homeostasis / cellular response to nutrient levels / negative regulation of lipid catabolic process / response to UV / Activation of AMPK downstream of NMDARs / cellular response to glucose starvation / energy homeostasis / positive regulation of protein localization / positive regulation of autophagy / positive regulation of adipose tissue development / negative regulation of TORC1 signaling / 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 / response to gamma radiation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of D-glucose import / TP53 Regulates Metabolic Genes / cellular response to glucose stimulus / regulation of circadian rhythm / ADP binding / response to hydrogen peroxide / autophagy / positive regulation of T cell activation / cellular response to hydrogen peroxide / Wnt signaling pathway / neuron cellular homeostasis / response to estrogen / glucose metabolic process / fatty acid biosynthetic process / rhythmic process / cellular response to prostaglandin E stimulus / glucose homeostasis / cellular response to xenobiotic stimulus / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity
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 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 / Resolution: 2.285 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-2
C: 5'-AMP-activated protein kinase subunit gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4606
Polymers59,4193
Non-polymers1,0423
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-38 kcal/mol
Surface area21190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.594, 115.334, 48.522
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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-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
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.26
Details: MES, 16% IPP, 1% 1,4-butanediol, pH 6.26, 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
ReflectionResolution: 2.285→30 Å / Num. all: 25462 / Num. obs: 24647 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 34.29 Å2
Reflection shellResolution: 2.285→2.34 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.23 / % possible all: 91.5

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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: 2.285→29.547 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8247 / SU ML: 0.31 / σ(F): 0.06 / Phase error: 24.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1172 5.06 %random
Rwork0.194 ---
all0.1969 25462 --
obs0.1969 23163 90.57 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.799 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso max: 173.9 Å2 / Biso mean: 46.9494 Å2 / Biso min: 11.38 Å2
Baniso -1Baniso -2Baniso -3
1-9.3533 Å2-0 Å2-0 Å2
2---2.0753 Å20 Å2
3----7.278 Å2
Refinement stepCycle: LAST / Resolution: 2.285→29.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3544 0 69 102 3715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043694
X-RAY DIFFRACTIONf_angle_d0.9085017
X-RAY DIFFRACTIONf_chiral_restr0.055591
X-RAY DIFFRACTIONf_plane_restr0.004604
X-RAY DIFFRACTIONf_dihedral_angle_d17.1811341
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2849-2.38890.30381340.24852273240777
2.3889-2.51480.27631250.2262567269285
2.5148-2.67220.27181460.21062658280490
2.6722-2.87840.28121570.20472783294092
2.8784-3.16770.25971560.19672813296994
3.1677-3.62540.27221480.1872925307396
3.6254-4.56490.19521520.16092952310496
4.5649-29.54980.24981540.19463020317494
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)
11.71520.12110.85111.1019-0.0871.03850.0046-0.09760.19170.21970.06750.319-0.5542-0.27120.13660.0844-0.1653-0.1837-0.0295-0.12080.14583.880939.2871-13.5484
20.03480.3104-0.15263.0236-1.90251.81960.344-0.0350.47780.0073-0.3405-0.1823-0.02010.4830.04040.026-0.00660.00280.11970.05790.42110.641928.7851-18.6338
31.9826-2.52410.41435.499-0.61390.7847-0.20840.2776-0.0620.4091-0.01240.1292-0.12270.04250.22550.1288-0.019-0.05450.13040.0130.23970.387536.4146-20.9768
42.14422.09850.33772.08810.11960.7819-0.09690.0112-0.32170.0903-0.0414-0.55820.0501-0.02430.05780.09870.0199-0.04260.0983-0.02750.16072.045726.6322-11.7315
54.64633.63530.95063.72230.67250.59610.0434-0.09520.6105-0.4926-0.34260.36590.04730.04080.33080.3328-0.0772-0.12510.35390.07930.5176-3.588944.0105-27.2138
62.33071.26081.07392.4631-1.32382.52880.2023-0.02250.59850.0785-0.05820.51710.43940.2028-0.12670.26910.0519-0.07290.1350.03040.3359-13.331334.7628-22.6496
70.29590.39451.00242.2870.55583.8055-0.12220.0336-0.0032-0.0193-0.08-0.3933-0.15510.38980.1550.0755-0.03920.02020.11370.00480.1392-7.436430.5676-19.0715
80.1551-0.04780.2790.0149-0.08330.49750.2534-0.09650.2133-0.2561-0.18030.09450.05370.0199-0.08150.48970.0104-0.00240.3192-0.14920.3307-9.84730.4925-2.3433
90.36530.09370.11380.4518-0.27510.2611-0.130.0410.0335-0.1216-0.1427-0.0216-0.05560.11040.19140.13-0.00870.02260.1507-0.03020.0796-7.120421.0839-19.4253
100.23520.06760.14050.2804-0.24830.3507-0.0406-0.0555-0.00630.0645-0.0502-0.0075-0.0515-0.06140.04880.09160.036-0.01690.1021-0.02090.0769-12.782510.8941-8.1631
110.5643-0.5907-0.36651.39980.68530.35610.4063-0.1031-0.0123-0.3879-0.42470.121-0.0908-0.54420.00630.358-0.1126-0.02230.3302-0.03310.0575-8.851111.94555.2964
121.18960.67770.14740.44550.45420.5771-0.0083-0.0416-0.0504-0.00930.0365-0.0920.3139-0.0974-0.02130.18760.0068-0.0250.0751-0.00670.0737-18.5743-1.3887-16.4731
130.48210.38420.65170.64790.92341.8423-0.1876-0.41130.0215-0.039-0.26320.033-0.022-0.59550.37080.12220.0595-0.07570.3068-0.16010.1336-32.84925.3928-2.7993
140.76410.01730.05540.69130.14041.21610.29560.2696-0.07910.51410.4116-0.0906-0.2051-0.0691-0.63281.0736-0.059-0.23190.7381-0.03670.5313-36.78612.5655-12.0587
150.98580.5873-0.15751.02530.33820.39620.13520.1023-0.0076-0.1245-0.2102-0.01260.154-0.19240.0540.1794-0.0707-0.02750.1802-0.030.1154-30.6575-5.8549-17.9458
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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