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- PDB-4red: Crystal structure of human AMPK alpha1 KD-AID with K43A mutation -

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Basic information

Entry
Database: PDB / ID: 4red
TitleCrystal structure of human AMPK alpha1 KD-AID with K43A mutation
Components5'-AMP-activated protein kinase catalytic subunit alpha-1
KeywordsTRANSFERASE / Kinase Domain Fold / phosphorylate numerous cellular targets / upregulate ATP-generating pathways upon activation / AMPK beta and gamma subunits
Function / homology
Function and homology information


negative regulation of glucosylceramide biosynthetic process / positive regulation of peptidyl-lysine acetylation / positive regulation of mitochondrial transcription / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / cold acclimation / lipid droplet disassembly / positive regulation of skeletal muscle tissue development / CAMKK-AMPK signaling cascade ...negative regulation of glucosylceramide biosynthetic process / positive regulation of peptidyl-lysine acetylation / positive regulation of mitochondrial transcription / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / cold acclimation / lipid droplet disassembly / positive regulation of skeletal muscle tissue development / CAMKK-AMPK signaling cascade / regulation of vesicle-mediated transport / nucleotide-activated protein kinase complex / Energy dependent regulation of mTOR by LKB1-AMPK / positive regulation of T cell mediated immune response to tumor cell / tau-protein kinase / negative regulation of hepatocyte apoptotic process / cellular response to ethanol / negative regulation of TOR signaling / response to caffeine / positive regulation of protein targeting to mitochondrion / cAMP-dependent protein kinase activity / protein localization to lipid droplet / motor behavior / tau-protein kinase activity / lipid biosynthetic process / negative regulation of tubulin deacetylation / Macroautophagy / cellular response to stress / cholesterol biosynthetic process / 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 / Activation of AMPK downstream of NMDARs / energy homeostasis / positive regulation of protein localization / positive regulation of adipose tissue development / negative regulation of TORC1 signaling / positive regulation of autophagy / 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 / TP53 Regulates Metabolic Genes / positive regulation of cholesterol biosynthetic process / cellular response to glucose stimulus / regulation of circadian rhythm / tau protein binding / 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 / 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 / response to hypoxia / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / nuclear speck / ciliary basal body / cilium / protein phosphorylation / apical plasma membrane / axon / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body
Similarity search - Function
PRKAA1, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase alpha 1 catalytic subunit, C-terminal / : / AMP-activated protein kinase, alpha subunit, autoinhibitory domain / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / KA1 domain/Ssp2, C-terminal / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 ...PRKAA1, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase alpha 1 catalytic subunit, C-terminal / : / AMP-activated protein kinase, alpha subunit, autoinhibitory domain / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / KA1 domain/Ssp2, C-terminal / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5'-AMP-activated protein kinase catalytic subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsZhou, X.E. / Ke, J. / Li, X. / Wang, L. / Gu, X. / de Waal, P.W. / Tan, M.H.E. / Wang, D. / Wu, D. / Xu, H.E. / Melcher, K.
CitationJournal: Cell Res. / Year: 2015
Title: Structural basis of AMPK regulation by adenine nucleotides and glycogen.
Authors: Li, X. / Wang, L. / Zhou, X.E. / Ke, J. / de Waal, P.W. / Gu, X. / Tan, M.H. / Wang, D. / Wu, D. / Xu, H.E. / Melcher, K.
History
DepositionSep 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Mar 11, 2015Group: Structure summary
Revision 1.3Sep 20, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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 catalytic subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)80,4002
Polymers80,4002
Non-polymers00
Water54030
1
A: 5'-AMP-activated protein kinase catalytic subunit alpha-1
B: 5'-AMP-activated protein kinase catalytic subunit alpha-1

A: 5'-AMP-activated protein kinase catalytic subunit alpha-1
B: 5'-AMP-activated protein kinase catalytic subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)160,8014
Polymers160,8014
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_455-x-1,-y,z1
Buried area17360 Å2
ΔGint-94 kcal/mol
Surface area58040 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-25 kcal/mol
Surface area33260 Å2
MethodPISA
3
A: 5'-AMP-activated protein kinase catalytic subunit alpha-1

B: 5'-AMP-activated protein kinase catalytic subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)80,4002
Polymers80,4002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_455-x-1,-y,z1
Buried area3700 Å2
ΔGint-20 kcal/mol
Surface area34000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.532, 119.532, 215.639
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.221744, -0.975105, 0.000106), (-0.975101, 0.221743, 0.002865), (-0.002818, 0.000532, -0.999996)-72.72817, -58.13783, 11.14912

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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: 40200.234 Da / Num. of mol.: 2 / Fragment: human AMPK KD-AID, UNP residues 22-362 / Mutation: K43A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMPK Alpha1 (11-353), AMPK1, PRKAA1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q13131, non-specific serine/threonine protein kinase, EC: 2.7.11.27, [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase, tau-protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.4 Å3/Da / Density % sol: 48.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.5 M HNa2PO4/0.5 M HK2PO4, 0.1 M Tris hydrochloride, pH 8.5, 0.1 M H(NH4)2PO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07806 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 13, 2012
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07806 Å / Relative weight: 1
ReflectionResolution: 2.95→30 Å / Num. all: 16876 / Num. obs: 16876 / % possible obs: 100 % / Redundancy: 17.3 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 32.3
Reflection shellResolution: 2.95→3.06 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H6D

2h6d


Resolution: 2.95→29.9 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.897 / SU B: 19.358 / SU ML: 0.363 / Cross valid method: THROUGHOUT / ESU R Free: 0.489 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27681 1222 7.3 %RANDOM
Rwork0.2297 ---
obs0.23312 15630 99.75 %-
all-15669 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.763 Å2
Baniso -1Baniso -2Baniso -3
1--2.01 Å20 Å2-0 Å2
2---2.01 Å20 Å2
3---4.03 Å2
Refinement stepCycle: LAST / Resolution: 2.95→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5293 0 0 30 5323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195412
X-RAY DIFFRACTIONr_bond_other_d0.0110.025212
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9697315
X-RAY DIFFRACTIONr_angle_other_deg0.89312027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7995654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60423.92250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.65415971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0841532
X-RAY DIFFRACTIONr_chiral_restr0.0690.2806
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216006
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021218
X-RAY DIFFRACTIONr_mcbond_it4.7877.1292631
X-RAY DIFFRACTIONr_mcbond_other4.7877.1292630
X-RAY DIFFRACTIONr_mcangle_it7.38410.6883280
X-RAY DIFFRACTIONr_mcangle_other7.38310.6883281
X-RAY DIFFRACTIONr_scbond_it4.8637.5482778
X-RAY DIFFRACTIONr_scbond_other4.8567.5482778
X-RAY DIFFRACTIONr_scangle_other7.38611.1854035
X-RAY DIFFRACTIONr_long_range_B_refined12.42666.79421526
X-RAY DIFFRACTIONr_long_range_B_other12.42566.79421526
LS refinement shellResolution: 2.949→3.025 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 86 -
Rwork0.288 1122 -
obs--99.42 %

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