[English] 日本語
Yorodumi
- PDB-5ufu: Structure of AMPK bound to activator -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ufu
TitleStructure of AMPK bound to activator
Components
  • (5'-AMP-activated protein kinase subunit ...) x 2
  • 5'-AMP-activated protein kinase catalytic subunit alpha-1
KeywordsTRANSFERASE/ACTIVATOR / Kinase / AMPK / activator / allostery / TRANSFERASE-ACTIVATOR complex
Function / homology
Function and homology information


bile acid signaling pathway / : / regulation of peptidyl-serine phosphorylation / Energy dependent regulation of mTOR by LKB1-AMPK / eukaryotic elongation factor-2 kinase activator activity / regulation of bile acid secretion / positive regulation of peptidyl-lysine acetylation / Macroautophagy / Energy dependent regulation of mTOR by LKB1-AMPK / Regulation of TP53 Activity through Phosphorylation ...bile acid signaling pathway / : / regulation of peptidyl-serine phosphorylation / Energy dependent regulation of mTOR by LKB1-AMPK / eukaryotic elongation factor-2 kinase activator activity / regulation of bile acid secretion / positive regulation of peptidyl-lysine acetylation / Macroautophagy / 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 / TP53 Regulates Metabolic Genes / 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 / Regulation of TP53 Activity through Phosphorylation / 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 / tau-protein kinase activity / lipid biosynthetic process / negative regulation of tubulin deacetylation / bile acid and bile salt transport / 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 / negative regulation of insulin receptor signaling pathway / positive regulation of protein localization / positive regulation of autophagy / positive regulation of adipose tissue development / negative regulation of TORC1 signaling / positive regulation of gluconeogenesis / 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 / Wnt signaling pathway / autophagy / positive regulation of T cell activation / kinase binding / cellular response to hydrogen peroxide / 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 / ciliary basal body / 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
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 / 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. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-85V / ADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / STAUROSPORINE / 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 / 5'-AMP-activated protein kinase catalytic subunit alpha-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.45 Å
AuthorsCalabrese, M.F. / Kurumbail, R.G.
CitationJournal: Cell Metab. / Year: 2017
Title: Activation of Skeletal Muscle AMPK Promotes Glucose Disposal and Glucose Lowering in Non-human Primates and Mice.
Authors: Cokorinos, E.C. / Delmore, J. / Reyes, A.R. / Albuquerque, B. / Kjbsted, R. / Jrgensen, N.O. / Tran, J.L. / Jatkar, A. / Cialdea, K. / Esquejo, R.M. / Meissen, J. / Calabrese, M.F. / Cordes, ...Authors: Cokorinos, E.C. / Delmore, J. / Reyes, A.R. / Albuquerque, B. / Kjbsted, R. / Jrgensen, N.O. / Tran, J.L. / Jatkar, A. / Cialdea, K. / Esquejo, R.M. / Meissen, J. / Calabrese, M.F. / Cordes, J. / Moccia, R. / Tess, D. / Salatto, C.T. / Coskran, T.M. / Opsahl, A.C. / Flynn, D. / Blatnik, M. / Li, W. / Kindt, E. / Foretz, M. / Viollet, B. / Ward, J. / Kurumbail, R.G. / Kalgutkar, A.S. / Wojtaszewski, J.F.P. / Cameron, K.O. / Miller, R.A.
History
DepositionJan 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)120,58813
Polymers118,2593
Non-polymers2,33010
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12020 Å2
ΔGint-130 kcal/mol
Surface area35850 Å2
MethodPISA
2
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

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)241,17626
Polymers236,5176
Non-polymers4,65920
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area27290 Å2
ΔGint-271 kcal/mol
Surface area68460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.264, 124.264, 401.569
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

-
Components

-
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: 57779.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Mus musculus (house mouse)
Gene: Prkaa1, Ampk1, Prkaa1 / Production host: Escherichia coli (E. coli)
References: UniProt: P54645, UniProt: Q5EG47, non-specific serine/threonine protein kinase

-
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: 23045.273 Da / Num. of mol.: 1
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

-
Non-polymers , 6 types, 10 molecules

#4: Chemical ChemComp-STU / STAUROSPORINE


Mass: 466.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM
#5: Chemical ChemComp-85V / 1,4:3,6-dianhydro-2-O-(6-chloro-5-{4-[1-(hydroxymethyl)cyclopropyl]phenyl}-1H-benzimidazol-2-yl)-D-mannitol


Mass: 442.892 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H23ClN2O5
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#9: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

-
Details

Has protein modificationY
Sequence detailsENGINEERED INSERTION ASGGPGGS

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.79 Å3/Da / Density % sol: 67.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 750 mM ammonium sulfate 500 mM lithium sulfate 100 mM trisodium citrate 1% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.45→47.43 Å / Num. obs: 25121 / % possible obs: 99.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 91.98 Å2 / Rpim(I) all: 0.095 / Net I/σ(I): 9.9
Reflection shellResolution: 3.45→3.51 Å / CC1/2: 0.817 / Rpim(I) all: 35.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
BUSTER2.11.7refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.45→47.43 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.875 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 2.086 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.403 / SU Rfree Cruickshank DPI: 0.404
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1242 4.94 %RANDOM
Rwork0.193 ---
obs0.195 25121 99.9 %-
Displacement parametersBiso max: 212.29 Å2 / Biso mean: 90.7 Å2 / Biso min: 35.61 Å2
Baniso -1Baniso -2Baniso -3
1--9.1869 Å20 Å20 Å2
2---9.1869 Å20 Å2
3---18.3737 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 3.45→47.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5973 0 152 0 6125
Biso mean--115.6 --
Num. residues----817
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1929SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes102HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1047HARMONIC5
X-RAY DIFFRACTIONt_it6278HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion884SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7210SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6278HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg8634HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion2.42
X-RAY DIFFRACTIONt_other_torsion20.95
LS refinement shellResolution: 3.45→3.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.284 115 4.21 %
Rwork0.215 2617 -
all0.217 2732 -
obs--99.53 %
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)
10.11760.1085-0.1290.91070.74381.91310.07270.00580.0542-0.061-0.09740.1382-0.5063-0.18990.02480.17650.0512-0.022-0.022-0.1207-0.1143-32.01431.5377-16.276
21.4578-0.2718-1.3623-0.01060.84422.7153-0.01160.04130.2255-0.10840.0780.1547-0.5154-0.1536-0.06640.17440.110.011-0.0736-0.1038-0.1064-26.478239.8166-31.8294
33.1379-2.5261-0.834.29592.46953.8746-0.1376-0.81260.625-0.13560.8985-0.9516-0.29911.0079-0.7609-0.27980.12340.09960.1241-0.3796-0.0548-39.070166.655516.7461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A9 - 548
2X-RAY DIFFRACTION2{ B|* }B77 - 270
3X-RAY DIFFRACTION3{ C|* }C26 - 322

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more