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

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Basic information

Entry
Database: PDB / ID: 4eag
TitleCo-crystal structure of an chimeric AMPK core with ATP
Components
  • (5'-AMP-activated protein kinase subunit ...) x 2
  • EG:132E8.2 protein
KeywordsTRANSFERASE / AMPK
Function / homology
Function and homology information


triglyceride storage / regulation of digestive system process / AMPK inhibits chREBP transcriptional activation activity / Energy dependent regulation of mTOR by LKB1-AMPK / Nuclear events mediated by NFE2L2 / Carnitine shuttle / Regulation of TP53 Activity through Phosphorylation / TP53 Regulates Metabolic Genes / behavioral response to starvation / Macroautophagy ...triglyceride storage / regulation of digestive system process / AMPK inhibits chREBP transcriptional activation activity / Energy dependent regulation of mTOR by LKB1-AMPK / Nuclear events mediated by NFE2L2 / Carnitine shuttle / Regulation of TP53 Activity through Phosphorylation / TP53 Regulates Metabolic Genes / behavioral response to starvation / Macroautophagy / Energy dependent regulation of mTOR by LKB1-AMPK / Regulation of TP53 Activity through Phosphorylation / basolateral part of cell / Macroautophagy / TP53 Regulates Metabolic Genes / nail development / G protein-coupled receptor kinase activity / AMP-activated protein kinase activity / regulation of carbon utilization / import into nucleus / positive regulation of autophagosome assembly / nucleotide-activated protein kinase complex / establishment or maintenance of epithelial cell apical/basal polarity / negative regulation of cell size / protein kinase regulator activity / positive regulation of axon guidance / positive regulation of lipophagy / regulation of glycolytic process / protein localization to lipid droplet / dendrite morphogenesis / AMP binding / positive regulation of macroautophagy / cellular response to nutrient levels / cellular response to glucose starvation / negative regulation of TORC1 signaling / positive regulation of TORC1 signaling / positive regulation of gluconeogenesis / positive regulation of autophagy / cellular response to starvation / regulation of cell growth / ADP binding / lipid metabolic process / fatty acid biosynthetic process / mitotic cell cycle / positive regulation of cold-induced thermogenesis / non-specific serine/threonine protein kinase / endosome / protein serine/threonine kinase activity / positive regulation of cell population proliferation / protein kinase binding / protein-containing complex binding / signal transduction / protein-containing complex / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Kinase associated domain 1, KA1 / : / 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 / : / 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 / non-specific serine/threonine protein kinase / 5'-AMP-activated protein kinase subunit gamma-1 / 5'-AMP-activated protein kinase subunit beta-1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 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 1.2Nov 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EG:132E8.2 protein
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)63,3046
Polymers62,1263
Non-polymers1,1783
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8490 Å2
ΔGint-42 kcal/mol
Surface area21170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.668, 151.283, 109.323
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein EG:132E8.2 protein / FI03728p / SNF1A/AMP-activated protein kinase / SNF1A/AMP-activated protein kinase / isoform A / ...FI03728p / SNF1A/AMP-activated protein kinase / SNF1A/AMP-activated protein kinase / isoform A / SNF1A/AMP-activated protein kinase / isoform B / SNF1A/AMP-activated protein kinase / isoform C


Mass: 14897.316 Da / Num. of mol.: 1 / Fragment: UNP residues 458-582
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: SNF1A, EG:132E8.2, SNF1A-RA, CG3051, Dmel_CG3051 / Production host: Escherichia coli (E. coli)
References: UniProt: O18645, Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases, G-protein-coupled receptor 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 / AMPK subunit beta-1 / AMPKb / 5'-AMP-activated protein kinase 40 kDa subunit


Mass: 9794.592 Da / Num. of mol.: 1 / Fragment: UNP residues 187-270
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 / AMPK gamma1 / AMPK 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, 84 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.: 81 / 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: 3.62 Å3/Da / Density % sol: 65.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.02
Details: MES, 12% Methanol, 2% 1,4-butanodiol, pH 6.02 , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: 2.7→30 Å / Num. all: 25106 / Num. obs: 19457 / % possible obs: 77.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 33.36 Å2
Reflection shellResolution: 2.7→2.75 Å / % possible all: 15.1

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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: 2.701→29.861 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7914 / SU ML: 0.33 / σ(F): 1.35 / Phase error: 27.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2521 982 5.05 %random
Rwork0.2083 ---
all0.2106 25106 --
obs0.2106 19448 77.62 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.859 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso max: 165.73 Å2 / Biso mean: 44.3536 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1--4.1823 Å2-0 Å2-0 Å2
2---10.6293 Å20 Å2
3----5.8532 Å2
Refinement stepCycle: LAST / Resolution: 2.701→29.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3601 0 73 81 3755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093748
X-RAY DIFFRACTIONf_angle_d1.3485081
X-RAY DIFFRACTIONf_chiral_restr0.083598
X-RAY DIFFRACTIONf_plane_restr0.006604
X-RAY DIFFRACTIONf_dihedral_angle_d20.6371368
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7009-2.84320.299480.214889093827
2.8432-3.02120.2691860.23741724181051
3.0212-3.25420.30051230.24912410253372
3.2542-3.58120.3091700.23273155332593
3.5812-4.09820.25161710.195733853556100
4.0982-5.1590.18651930.163334093602100
5.159-29.86250.25551910.22233493368499
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)
10.0001-0.0125-0.00570.01430.0031-0.0103-0.00650.04720.0335-0.00560.0311-0.0432-0.15250.007100.15050.30380.07850.08370.12640.2073-60.0422-11.69876.8957
20.0028-0.0009-0.00070.00110.00070.0035-0.00310.0002-0.0039-0.00370.0091-0.0028-0.00630.0018-00.17090.18930.03750.168-0.05010.2327-62.6022-24.090710.2762
30.0085-0.0024-0.00080.0027-0.01120.01060.04220.13680.0485-0.0217-0.0025-0.02190.01660.0105-00.13230.2029-0.04960.09410.17620.0135-57.4971-15.807910.5462
40.01710.00590.00780.0049-0.0022-0.00660.06690.0917-0.0334-0.07770.07690.0216-0.1164-0.04640-0.08190.27350.0052-0.29890.06550.026-52.1316-23.95717.9899
50.00340.00410.0053-0.00530.0105-0.00380.04840.0271-0.09270.01690.04640.03050.0414-0.0224-00.35810.282-0.05810.3444-0.06070.4461-59.581-3.95715.859
60.00010.0002-0.00040.001-0.0006-0.00050.0049-0.0019-0.0030.0039-0.001-0.00270.0009-0.0114-00.495-0.00770.05750.42820.04290.527-42.8199-6.800616.2999
70.00540.0064-0.00060.0176-0.00290.001-0.00350.00130.00130.0025-0.00420.0003-0.0003-0.0025-00.41380.03740.02420.3591-0.12080.3878-43.3056-13.014425.1009
8-0.004-0.013-0.0130.00790.00280.0019-0.06410.04260.181-0.07890.00490.0376-0.02930.03190-0.13960.09310.379-0.0415-0.0339-0.4452-43.827-19.705412.9155
90.05480.00270.0256-0.0116-0.02390.00730.16430.0508-0.0607-0.0263-0.2442-0.0434-0.00730.10080-0.18980.01530.1565-0.0548-0.1246-0.496-32.157-31.83027.3449
100.0048-0.0053-0.0021-0.0006-0.00230.00370.00780.06550.0112-0.00790.004-0.01220.04330.006900.01840.0955-0.05640.1678-0.04750.0548-34.4054-34.2942-5.6615
11-0.0064-0.02550.0265-0.0239-0.016-0.03450.0024-0.22520.00870.0059-0.04070.10350.1810.41960-0.98770.74210.0159-0.94610.1045-0.0922-27.4742-40.756222.21
12-0.0024-0.0005-0.0018-0.0141-0.0073-0.00110.01750.05960.05140.03910.01290.00660.02730.08720-0.33660.02630.02830.1581-0.0339-0.0311-10.283-34.25611.7213
130.00350.0007-0.01050.00020.0058-0.0080.02020.00910.0475-0.0629-0.0340.0198-0.10750.2341-0-0.49140.48160.237-0.2716-0.2578-0.0189-11.5151-37.931420.0859
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 458:496)A458 - 496
2X-RAY DIFFRACTION2(chain A and resid 497:500)A497 - 500
3X-RAY DIFFRACTION3(chain A and resid 501:526)A501 - 526
4X-RAY DIFFRACTION4(chain A and resid 527:582)A527 - 582
5X-RAY DIFFRACTION5(chain B and resid 191:207)B191 - 207
6X-RAY DIFFRACTION6(chain B and resid 211:215)B211 - 215
7X-RAY DIFFRACTION7(chain B and resid 220:233)B220 - 233
8X-RAY DIFFRACTION8(chain B and resid 234:270)B234 - 270
9X-RAY DIFFRACTION9(chain C and resid 26:106)C26 - 106
10X-RAY DIFFRACTION10(chain C and resid 107:125)C107 - 125
11X-RAY DIFFRACTION11(chain C and resid 126:202)C126 - 202
12X-RAY DIFFRACTION12(chain C and resid 203:265)C203 - 265
13X-RAY DIFFRACTION13(chain C and resid 266:324)C266 - 324

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