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- PDB-4eak: Co-crystal structure of an AMPK core with ATP -

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Basic information

Entry
Database: PDB / ID: 4eak
TitleCo-crystal structure of an AMPK core 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 / Regulation of TP53 Activity through Phosphorylation / Macroautophagy / TP53 Regulates Metabolic Genes / positive regulation of mitochondrial transcription / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / nail development / [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 / Regulation of TP53 Activity through Phosphorylation / Macroautophagy / TP53 Regulates Metabolic Genes / positive regulation of mitochondrial transcription / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / cold acclimation / 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 / positive regulation of fatty acid oxidation / positive regulation of T cell mediated immune response to tumor cell / tau-protein kinase / negative regulation of hepatocyte apoptotic process / cellular response to ethanol / 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 / motor behavior / lipid biosynthetic process / negative regulation of tubulin deacetylation / 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 / 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 / response to gamma radiation / positive regulation of D-glucose import / 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 / 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 / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / negative regulation of translation / nuclear speck / ciliary basal body / protein phosphorylation / apical plasma membrane
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-5'-TRIPHOSPHATE / 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: 2.5 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)58,8436
Polymers57,6663
Non-polymers1,1783
Water1,33374
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-29 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.558, 40.508, 77.598
Angle α, β, γ (deg.)90.000, 105.110, 90.000
Int Tables number5
Space group name H-MC121

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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, EC: 2.7.11.27, [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-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

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Non-polymers , 3 types, 77 molecules

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


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 0.1M MES pH 5.9, 18% IPP, VAPOR DIFFUSION, HANGING DROP, temperature 298 K

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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: Mar 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 18796 / Num. obs: 18796 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 57.2 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 13.11
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

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

2v8q


Resolution: 2.5→28.631 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.39 / σ(F): 0.13 / Phase error: 26.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2543 908 5.07 %random
Rwork0.2373 ---
obs0.2382 17922 95.15 %-
all-18796 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.49 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso max: 169.36 Å2 / Biso mean: 72.9033 Å2 / Biso min: 25.54 Å2
Baniso -1Baniso -2Baniso -3
1-3.9011 Å20 Å2-7.3909 Å2
2--5.5209 Å20 Å2
3----9.4219 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3389 0 73 74 3536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093530
X-RAY DIFFRACTIONf_angle_d0.9644791
X-RAY DIFFRACTIONf_chiral_restr0.055567
X-RAY DIFFRACTIONf_plane_restr0.008574
X-RAY DIFFRACTIONf_dihedral_angle_d19.7431293
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 (%)
2.4971-2.65340.28761350.26662520265586
2.6534-2.85810.28781440.26432709285392
2.8581-3.14540.28321220.24672849297196
3.1454-3.59980.2681760.23122900307698
3.5998-4.53250.20261660.20332971313799
4.5325-28.63280.25291650.239230653230100
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)
12.895-0.2240.19410.57440.32770.6541-0.13020.0051-0.6701-0.2228-0.43120.0103-0.25750.3030.37680.5288-0.0203-0.13070.86580.32850.628330.1286395.6968-20.6769
2-0.002-0.020.01380.647-0.23420.0823-0.0652-0.54240.2191-0.0128-0.2844-0.4221-0.45120.98020.24510.434-0.2642-0.25581.5940.2710.608435.7301402.6054-11.4011
31.51480.7791-1.42272.0732-0.11792.8695-0.0953-1.0594-0.06690.31130.02120.3322-0.08071.3608-0.03780.5308-0.1987-0.16461.25140.00640.622126.3628403.4301-4.1787
40.8080.8085-0.51781.0575-1.24151.82920.24630.1701-0.54220.4778-1.0302-0.184-0.71860.75330.4510.6366-0.0956-0.0870.81060.23990.518325.9462396.6461-10.6189
51.83710.7637-0.5570.5594-0.52280.52980.2269-0.8023-0.4644-0.1153-0.02240.47560.20310.09-0.3660.3472-0.0413-0.09170.58440.21530.706524.4307393.6037-11.4138
61.13580.0738-0.63161.3003-0.17280.79360.1222-0.40790.02080.5446-0.0198-0.05780.00890.4721-0.12140.2827-0.1129-0.0220.3175-0.0230.215318.7494403.6304-13.4959
70.7998-1.0416-0.00793.19360.52162.2822-0.67630.0089-0.1547-0.1548-0.47131.37780.35650.04430.55990.97230.40450.04680.65880.13910.982127.2496385.7075-13.1832
81.2965-0.66540.8542.2287-0.20391.11140.4989-0.0866-0.3416-0.6441-0.0957-0.26860.1061-0.1594-0.15130.62020.024-0.06610.44640.08770.517518.4796392.6997-17.8311
90.671-0.50480.44061.0293-0.50031.89740.1713-0.0306-0.2709-0.0511-0.40190.249-0.04910.50360.24210.54160.04110.06740.43130.03280.399314.6763398.0009-20.961
100.49730.8149-0.10431.4089-0.53830.15980.15730.1024-0.21640.0653-0.1441-0.1912-0.0162-0.0258-0.09350.23910.05970.01020.26180.0080.3698.7105393.9159-15.7158
110.82250.1448-0.1789-0.0717-0.44140.39280.0634-0.06150.0286-0.1285-0.0240.0258-0.0643-0.0134-0.00420.3470.01740.02040.1925-0.04990.2257-2.5397398.1005-19.2701
122.1605-0.19810.25940.0181-0.06080.38030.01240.00030.7625-0.95740.04350.022-0.24240.06110.01311.02930.05130.24250.4650.06550.8367-0.4615416.4443-31.8801
130.48050.07690.28130.3753-0.39080.52340.046-0.10360.1014-0.0355-0.0952-0.1144-0.0818-0.10020.05120.20280.04370.04330.149-0.06970.1937-7.6289398.3392-15.1504
142.92470.9606-1.12121.3310.90541.91421.13730.70480.80480.71790.33640.4195-0.0191-1.0687-0.09940.5528-0.3172-0.32020.9779-0.22920.3747-29.2132381.7267-19.5384
151.05220.4047-0.08420.94050.21540.87650.14670.1694-0.1751-0.0194-0.22210.0604-0.3966-0.36010.11630.32950.1477-0.0530.4292-0.0690.3108-19.0559403.8841-37.1389
160.2362-0.0736-0.52860.4022-0.13721.47120.09480.2934-0.0574-0.3485-0.1147-0.02390.3694-0.3535-0.0210.3051-0.0739-0.05760.4572-0.00350.2849-17.7087393.1943-36.9261
170.709-0.2193-0.36390.7324-0.46850.6593-0.34990.6421-0.17280.07640.3341-0.2254-0.0156-0.7072-0.12070.2309-0.04690.0360.7146-0.04840.3563-25.1702392.6125-28.0591
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 396:406)A396 - 406
2X-RAY DIFFRACTION2(chain A and resid 407:414)A407 - 414
3X-RAY DIFFRACTION3(chain A and resid 415:439)A415 - 439
4X-RAY DIFFRACTION4(chain A and resid 440:458)A440 - 458
5X-RAY DIFFRACTION5(chain A and resid 459:467)A459 - 467
6X-RAY DIFFRACTION6(chain A and resid 529:548)A529 - 548
7X-RAY DIFFRACTION7(chain B and resid 202:235)B202 - 235
8X-RAY DIFFRACTION8(chain B and resid 236:243)B236 - 243
9X-RAY DIFFRACTION9(chain B and resid 244:256)B244 - 256
10X-RAY DIFFRACTION10(chain B and resid 257:270)B257 - 270
11X-RAY DIFFRACTION11(chain C and resid 23:94)C23 - 94
12X-RAY DIFFRACTION12(chain C and resid 95:111)C95 - 111
13X-RAY DIFFRACTION13(chain C and resid 112:180)C112 - 180
14X-RAY DIFFRACTION14(chain C and resid 181:196)C181 - 196
15X-RAY DIFFRACTION15(chain C and resid 197:251)C197 - 251
16X-RAY DIFFRACTION16(chain C and resid 252:296)C252 - 296
17X-RAY DIFFRACTION17(chain C and resid 297:324)C297 - 324

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