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- PDB-2v9j: Crystal structure of the regulatory fragment of mammalian AMPK in... -

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Basic information

Entry
Database: PDB / ID: 2v9j
TitleCrystal structure of the regulatory fragment of mammalian AMPK in complexes with Mg.ATP-AMP
Components
  • (5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT ...) x 2
  • 5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-1
KeywordsTRANSFERASE / ATP-BINDING / POLYMORPHISM / METAL-BINDING / SERINE/THREONINE-PROTEIN KINASE / KINASE / MAGNESIUM / CBS DOMAIN / STEROL BIOSYNTHESIS / STEROID BIOSYNTHESIS / FATTY ACID BIOSYNTHESIS / CHOLESTEROL BIOSYNTHESIS / LIPID SYNTHESIS / PHOSPHORYLATION / NUCLEOTIDE-BINDING
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 / histone H2BS36 kinase activity ...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 / import into nucleus / CAMKK-AMPK signaling cascade / regulation of vesicle-mediated transport / nucleotide-activated protein kinase complex / : / Energy dependent regulation of mTOR by LKB1-AMPK / Carnitine shuttle / tau-protein kinase / negative regulation of hepatocyte apoptotic process / protein kinase regulator activity / cellular response to ethanol / negative regulation of TOR signaling / protein localization to lipid droplet / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / response to caffeine / motor behavior / bile acid and bile salt transport / positive regulation of protein targeting to mitochondrion / lipid biosynthetic process / AMP-activated protein kinase activity / negative regulation of tubulin deacetylation / tau-protein kinase activity / Macroautophagy / cholesterol biosynthetic process / AMP binding / fatty acid oxidation / fatty acid homeostasis / negative regulation of lipid catabolic process / cellular response to nutrient levels / positive regulation of autophagy / cellular response to glucose starvation / regulation of microtubule cytoskeleton organization / Activation of AMPK downstream of NMDARs / response to UV / positive regulation of protein localization / energy homeostasis / positive regulation of gluconeogenesis / negative regulation of insulin receptor signaling pathway / negative regulation of TORC1 signaling / positive regulation of adipose tissue development / positive regulation of glycolytic process / cellular response to calcium ion / response to gamma radiation / response to activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of D-glucose import / TP53 Regulates Metabolic Genes / cellular response to glucose stimulus / ADP binding / regulation of circadian rhythm / response to hydrogen peroxide / Wnt signaling pathway / autophagy / fatty acid biosynthetic process / cellular response to hydrogen peroxide / response to estrogen / neuron cellular homeostasis / glucose metabolic process / cellular response to prostaglandin E stimulus / rhythmic process / cellular response to xenobiotic stimulus / positive regulation of cold-induced thermogenesis / glucose homeostasis / 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 / nuclear speck / response to xenobiotic stimulus / protein phosphorylation / apical plasma membrane / axon / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / chromatin binding / positive regulation of cell population proliferation / dendrite
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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsXiao, B. / Heath, R. / Saiu, P. / Leiper, F.C. / Leone, P. / Jing, C. / Walker, P.A. / Haire, L. / Eccleston, J.F. / Davis, C.T. ...Xiao, B. / Heath, R. / Saiu, P. / Leiper, F.C. / Leone, P. / Jing, C. / Walker, P.A. / Haire, L. / Eccleston, J.F. / Davis, C.T. / Martin, S.R. / Carling, D. / Gamblin, S.J.
CitationJournal: Nature / Year: 2007
Title: Structural Basis for AMP Binding to Mammalian AMP-Activated Protein Kinase
Authors: Xiao, B. / Heath, R. / Saiu, P. / Leiper, F.C. / Leone, P. / Jing, C. / Walker, P.A. / Haire, L. / Eccleston, J.F. / Davis, C.T. / Martin, S.R. / Carling, D. / Gamblin, S.J.
History
DepositionAug 23, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
E: 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5218
Polymers65,1113
Non-polymers1,4105
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-50.1 kcal/mol
Surface area30580 Å2
MethodPQS
Unit cell
Length a, b, c (Å)48.790, 120.685, 127.069
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 ALPHA-1 CHAIN / AMP-ACTIVATED PROTEIN KINASE


Mass: 17635.799 Da / Num. of mol.: 1 / Fragment: RESIDUES 396-548
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P54645, non-specific serine/threonine protein kinase

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5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT ... , 2 types, 2 molecules BE

#2: Protein 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT BETA-2 / AMPK BETA-2 CHAIN / AMP-ACTIVATED PROTEIN KINASE


Mass: 10040.813 Da / Num. of mol.: 1 / Fragment: RESIDUES 187-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O43741
#3: Protein 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1 / AMPK GAMMA-1 CHAIN / AMPKG / AMP-ACTIVATED PROTEIN KINASE


Mass: 37434.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P80385

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Non-polymers , 4 types, 147 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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 61.83 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MULTIWIRE / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.53→20 Å / Num. obs: 25861 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.3

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OOX

2oox


Resolution: 2.53→20 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FIRST FOUR RESIDUES (GSMA) OF THE SEQUENCE OF CHAIN A ARE GENERATED FROM THE POST HIS-TAG CLEAVAGE THE FIRST RESIDUES (M) OF THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FIRST FOUR RESIDUES (GSMA) OF THE SEQUENCE OF CHAIN A ARE GENERATED FROM THE POST HIS-TAG CLEAVAGE THE FIRST RESIDUES (M) OF THE SEQUENCE OF CHAIN B IS GENERATED BY THE WAY IT WAS CLONED INTO THE VECTOR
RfactorNum. reflection% reflection
Rfree0.266 --
Rwork0.225 --
obs-25861 96.2 %
Refinement stepCycle: LAST / Resolution: 2.53→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3885 0 87 142 4114

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