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- PDB-4cfh: Structure of an active form of mammalian AMPK -

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Basic information

Entry
Database: PDB / ID: 4cfh
TitleStructure of an active form of mammalian AMPK
Components
  • (5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA- ...) x 2
  • (5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT ...) x 2
KeywordsTRANSFERASE / TRANSFERASE PHOSPHORYLATION / ACTIVE FORM / NUCLEOTIDE-BINDING / STAUROSPORINE-BINDING / SERINE/THREONINE-PROTEIN KINASE
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 / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / positive regulation of mitochondrial transcription / 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 / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / positive regulation of mitochondrial transcription / AMPK inhibits chREBP transcriptional activation activity / histone H2BS36 kinase activity / cold acclimation / AMP-activated protein kinase activity / 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 / negative regulation of hepatocyte apoptotic process / positive regulation of fatty acid oxidation / Energy dependent regulation of mTOR by LKB1-AMPK / Carnitine shuttle / positive regulation of T cell mediated immune response to tumor cell / tau-protein kinase / 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 / negative regulation of tubulin deacetylation / AMP binding / Macroautophagy / cholesterol biosynthetic process / lipid biosynthetic process / cellular response to stress / fatty acid oxidation / motor behavior / cellular response to ethanol / fatty acid homeostasis / negative regulation of lipid catabolic process / cellular response to nutrient levels / response to UV / cellular response to glucose starvation / energy homeostasis / Activation of AMPK downstream of NMDARs / positive regulation of protein localization / negative regulation of TORC1 signaling / positive regulation of adipose tissue development / positive regulation of gluconeogenesis / positive regulation of autophagy / negative regulation of insulin receptor signaling pathway / cellular response to calcium ion / regulation of microtubule cytoskeleton organization / positive regulation of glycolytic process / response to activity / response to gamma radiation / positive regulation of D-glucose import / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cellular response to glucose stimulus / response to hydrogen peroxide / regulation of circadian rhythm / neuron cellular homeostasis / ADP binding / positive regulation of T cell activation / autophagy / response to estrogen / Wnt signaling pathway / cellular response to xenobiotic stimulus / cellular response to hydrogen peroxide / glucose metabolic process / fatty acid biosynthetic process / rhythmic process / cellular response to prostaglandin E stimulus / glucose homeostasis / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / negative regulation of translation / nuclear speck / ciliary basal body / apical plasma membrane / response to xenobiotic stimulus / axon / negative regulation of gene expression / protein serine kinase activity / neuronal cell body / protein serine/threonine kinase activity / positive regulation of cell population proliferation / dendrite / chromatin binding
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 / : / 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 ...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 / 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
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / STAUROSPORINE / 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: 3.24 Å
AuthorsXiao, B. / Sanders, M.J. / Underwood, E. / Heath, R. / Mayer, F. / Carmena, D. / Jing, C. / Walker, P.A. / Eccleston, J.F. / Haire, L.F. ...Xiao, B. / Sanders, M.J. / Underwood, E. / Heath, R. / Mayer, F. / Carmena, D. / Jing, C. / Walker, P.A. / Eccleston, J.F. / Haire, L.F. / Saiu, P. / Howell, S.A. / Aasland, R. / Martin, S.R. / Carling, D. / Gamblin, S.J.
Citation
Journal: Nature / Year: 2011
Title: Structure of Mammalian Ampk and its Regulation by Adp
Authors: Xiao, B. / Sanders, M.J. / Underwood, E. / Heath, R. / Mayer, F. / Carmena, D. / Jing, C. / Walker, P.A. / Eccleston, J.F. / Haire, L.F. / Saiu, P. / Howell, S.A. / Aasland, R. / Martin, S.R. ...Authors: Xiao, B. / Sanders, M.J. / Underwood, E. / Heath, R. / Mayer, F. / Carmena, D. / Jing, C. / Walker, P.A. / Eccleston, J.F. / Haire, L.F. / Saiu, P. / Howell, S.A. / Aasland, R. / Martin, S.R. / Carling, D. / Gamblin, S.J.
History
DepositionNov 18, 2013Deposition site: PDBE / Processing site: PDBE
SupersessionDec 25, 2013ID: 2Y94
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 20, 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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 CATALYTIC SUBUNIT ALPHA-1
E: 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,9497
Polymers107,7884
Non-polymers1,1613
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13440 Å2
ΔGint-85.5 kcal/mol
Surface area40040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.917, 133.917, 141.896
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA- ... , 2 types, 2 molecules AC

#1: Protein 5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-1 / AMPK SUBUNIT ALPHA-1


Mass: 57248.484 Da / Num. of mol.: 1 / Fragment: RESIDUES 13-481
Source method: isolated from a genetically manipulated source
Details: PROTEASE RECOGNITION SITES WERE ENGINEERED INTO THE ALPHA SUBUNIT AT BOTH ENDS OF A LARGE FLEXIBLE LOOP IN THE C-TERMINAL REGION (RESIDUES 470 TO 524), RESIDUES 471 TO 523 WERE REMOVED FROM ...Details: PROTEASE RECOGNITION SITES WERE ENGINEERED INTO THE ALPHA SUBUNIT AT BOTH ENDS OF A LARGE FLEXIBLE LOOP IN THE C-TERMINAL REGION (RESIDUES 470 TO 524), RESIDUES 471 TO 523 WERE REMOVED FROM THE PROTEIN, RESIDUES 523 TO 548 ARE GIVEN AS CHAIN C
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P54645, non-specific serine/threonine protein kinase
#3: Protein/peptide 5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-1 / AMPK SUBUNIT ALPHA-1


Mass: 3064.600 Da / Num. of mol.: 1 / Fragment: RESIDUES 535-559
Source method: isolated from a genetically manipulated source
Details: PROTEASE RECOGNITION SITES WERE ENGINEERED INTO THE SUBUNIT ALPHA AT BOTH ENDS OF A LARGE FLEXIBLE LOOP IN THE C-TERMINAL REGION (RESIDUES 470 AND 524), RESIDUES 471 TO 523 WERE REMOVED FROM ...Details: PROTEASE RECOGNITION SITES WERE ENGINEERED INTO THE SUBUNIT ALPHA AT BOTH ENDS OF A LARGE FLEXIBLE LOOP IN THE C-TERMINAL REGION (RESIDUES 470 AND 524), RESIDUES 471 TO 523 WERE REMOVED FROM THE PROTEIN, RESIDUES 2 TO 470 ARE GIVEN AS CHAIN A
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


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
#4: Protein 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1 / AMPK SUBUNIT ALPHA-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) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P80385

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Non-polymers , 2 types, 3 molecules

#5: Chemical ChemComp-STU / STAUROSPORINE


Mass: 466.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: antibiotic*YM
#6: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM

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Details

Has protein modificationY
Sequence detailsU40819 IN PUBMED. THE 19 RESIDUES (MSHHHHHHSSGLEVLFQGP)AT THE N-TERMINAL ARE EXPRESSION TAG. ...U40819 IN PUBMED. THE 19 RESIDUES (MSHHHHHHSSGLEVLFQGP)AT THE N-TERMINAL ARE EXPRESSION TAG. RESIDUES 471 TO 523 ARE REMOVED TO FAVOUR CRYSTALLIZATION, THE 6 RESIDUES (LEVLFQ) ARE EXPRESSION TAG AT THIS SITE. M AT THE N-TERMINAL IS EXPRESSION TAG.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: CRYSTALS WERE GROWN BY THE HANGING DROP METHOD WITH RESERVOIR SOLUTION CONTAINING 8% ISOPROPANOL AND 5% MPD AS PRECIPITANT IN 0.1M TRIS AT PH 7.5 AT 18 DEGREES.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9791
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.24→29.53 Å / Num. obs: 18662 / % possible obs: 93.3 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12
Reflection shellResolution: 3.24→3.44 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2 / % possible all: 95.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2V8Q AND 2H6D

2v8q

2h6d


Resolution: 3.24→29.53 Å / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2677 989 5 %
Rwork0.2325 --
obs0.2343 19619 93.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.24→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6348 0 81 0 6429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.24-3.41060.35681460.34122683X-RAY DIFFRACTION96
3.4106-3.62390.29671520.28932682X-RAY DIFFRACTION96
3.6239-3.90320.28231400.26622669X-RAY DIFFRACTION95
3.9032-4.29490.27081310.23112679X-RAY DIFFRACTION94
4.2949-4.91390.2441540.21042637X-RAY DIFFRACTION93
4.9139-6.18170.29031340.23482679X-RAY DIFFRACTION93
6.1817-29.53330.24391320.20942601X-RAY DIFFRACTION85

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