[English] 日本語
Yorodumi
- PDB-5ezv: X-ray crystal structure of AMP-activated protein kinase alpha-2/a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ezv
TitleX-ray crystal structure of AMP-activated protein kinase alpha-2/alpha-1 RIM chimaera (alpha-2(1-347)/alpha-1(349-401)/alpha-2(397-end) beta-1 gamma-1) co-crystallized with C2 (5-(5-hydroxyl-isoxazol-3-yl)-furan-2-phosphonic acid)
Components
  • (5'-AMP-activated protein kinase subunit ...) x 2
  • 5'-AMP-activated protein kinase catalytic subunit alpha-2/alpha-1 RIM SWAP chimera
KeywordsTRANSFERASE / serine/threonine kinase / allosteric activation / nucleotide-binding
Function / homology
Function and homology information


negative regulation of glucosylceramide biosynthetic process / positive regulation of mitochondrial transcription / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / AMPK inhibits chREBP transcriptional activation activity / cold acclimation / positive regulation of peptidyl-lysine acetylation / cAMP-dependent protein kinase regulator activity ...negative regulation of glucosylceramide biosynthetic process / positive regulation of mitochondrial transcription / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / AMPK inhibits chREBP transcriptional activation activity / cold acclimation / positive regulation of peptidyl-lysine acetylation / cAMP-dependent protein kinase regulator 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 / Energy dependent regulation of mTOR by LKB1-AMPK / positive regulation of T cell mediated immune response to tumor cell / Carnitine shuttle / tau-protein kinase / negative regulation of hepatocyte apoptotic process / cellular response to ethanol / negative regulation of TOR signaling / protein kinase regulator activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / Nuclear events mediated by NFE2L2 / response to caffeine / regulation of glycolytic process / positive regulation of protein targeting to mitochondrion / cAMP-dependent protein kinase activity / protein localization to lipid droplet / motor behavior / cellular response to stress / tau-protein kinase activity / negative regulation of tubulin deacetylation / lipid biosynthetic process / Macroautophagy / response to muscle activity / AMP binding / cholesterol biosynthetic process / fatty acid oxidation / positive regulation of macroautophagy / positive regulation of protein kinase activity / regulation of macroautophagy / fatty acid homeostasis / cellular response to nutrient levels / negative regulation of lipid catabolic process / regulation of microtubule cytoskeleton organization / response to UV / cellular response to glucose starvation / Activation of AMPK downstream of NMDARs / positive regulation of protein localization / negative regulation of insulin receptor signaling pathway / energy homeostasis / positive regulation of autophagy / negative regulation of TORC1 signaling / positive regulation of adipose tissue development / positive regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / cellular response to calcium ion / positive regulation of glycolytic process / response to activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / response to gamma radiation / positive regulation of cholesterol biosynthetic process / cellular response to glucose stimulus / regulation of circadian rhythm / tau protein binding / ADP binding / Wnt signaling pathway / autophagy / cellular response to hydrogen peroxide / positive regulation of T cell activation / neuron cellular homeostasis / response to estrogen / glucose metabolic process / cytoplasmic stress granule / fatty acid biosynthetic process / cellular response to prostaglandin E stimulus / rhythmic process / cellular response to xenobiotic stimulus / glucose homeostasis / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / spermatogenesis / 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
Similarity search - Function
PRKAA2, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase catalytic subunit alpha-2, C-terminal / 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 / : ...PRKAA2, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase catalytic subunit alpha-2, C-terminal / 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. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-C1V / Chem-C2Z / STAUROSPORINE / 5'-AMP-activated protein kinase subunit gamma-1 / 5'-AMP-activated protein kinase catalytic subunit alpha-2 / 5'-AMP-activated protein kinase catalytic subunit alpha-1 / 5'-AMP-activated protein kinase subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsLangendorf, C.G. / Kemp, B.E.
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis of allosteric and synergistic activation of AMPK by furan-2-phosphonic derivative C2 binding.
Authors: Langendorf, C.G. / Ngoei, K.R. / Scott, J.W. / Ling, N.X. / Issa, S.M. / Gorman, M.A. / Parker, M.W. / Sakamoto, K. / Oakhill, J.S. / Kemp, B.E.
History
DepositionNov 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Sep 27, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-AMP-activated protein kinase catalytic subunit alpha-2/alpha-1 RIM SWAP chimera
B: 5'-AMP-activated protein kinase subunit beta-1
C: 5'-AMP-activated protein kinase catalytic subunit alpha-2/alpha-1 RIM SWAP chimera
D: 5'-AMP-activated protein kinase subunit beta-1
E: 5'-AMP-activated protein kinase subunit gamma-1
F: 5'-AMP-activated protein kinase subunit gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,84414
Polymers265,2666
Non-polymers2,5788
Water1,51384
1
A: 5'-AMP-activated protein kinase catalytic subunit alpha-2/alpha-1 RIM SWAP chimera
B: 5'-AMP-activated protein kinase subunit beta-1
E: 5'-AMP-activated protein kinase subunit gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,9227
Polymers132,6333
Non-polymers1,2894
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13800 Å2
ΔGint-85 kcal/mol
Surface area41600 Å2
MethodPISA
2
C: 5'-AMP-activated protein kinase catalytic subunit alpha-2/alpha-1 RIM SWAP chimera
D: 5'-AMP-activated protein kinase subunit beta-1
F: 5'-AMP-activated protein kinase subunit gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,9227
Polymers132,6333
Non-polymers1,2894
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14060 Å2
ΔGint-88 kcal/mol
Surface area41800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.608, 134.112, 141.287
Angle α, β, γ (deg.)90.000, 93.160, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AC

#1: Protein 5'-AMP-activated protein kinase catalytic subunit alpha-2/alpha-1 RIM SWAP chimera / AMPK subunit alpha-2 / Acetyl-CoA carboxylase kinase / ACACA kinase / Hydroxymethylglutaryl-CoA ...AMPK subunit alpha-2 / Acetyl-CoA carboxylase kinase / ACACA kinase / Hydroxymethylglutaryl-CoA reductase kinase / HMGCR kinase / AMPK subunit alpha-1 / Acetyl-CoA carboxylase kinase / ACACA kinase / Hydroxymethylglutaryl-CoA reductase kinase / HMGCR kinase / Tau-protein kinase PRKAA1


Mass: 63902.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAA2, AMPK, AMPK2, PRKAA1, AMPK1 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3)
References: UniProt: P54646, UniProt: Q13131, non-specific serine/threonine protein kinase, EC: 2.7.11.27, [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase

-
5'-AMP-activated protein kinase subunit ... , 2 types, 4 molecules BDEF

#2: Protein 5'-AMP-activated protein kinase subunit beta-1 / AMPKb


Mass: 30504.299 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAB1, AMPK / Plasmid: pCOLA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: Q9Y478
#3: Protein 5'-AMP-activated protein kinase subunit gamma-1 / AMPKg


Mass: 38225.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAG1 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: P54619

-
Non-polymers , 4 types, 92 molecules

#4: Chemical ChemComp-STU / STAUROSPORINE


Mass: 466.531 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM
#5: Chemical ChemComp-C1V / 3-[4-(2-hydroxyphenyl)phenyl]-4-oxidanyl-6-oxidanylidene-7H-thieno[2,3-b]pyridine-5-carbonitrile


Mass: 360.386 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H12N2O3S
#6: Chemical
ChemComp-C2Z / 5-(5-hydroxyl-isoxazol-3-yl)-furan-2-phosphonic acid / [5-(5-hydroxy-1,2-oxazol-3-yl)furan-2-yl]phosphonic acid


Mass: 231.099 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6NO6P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 8 % PEG 3350, 0.1 M MgCl2, 1.0 % glucose, 0.001 % cocamidopropyl betaine, 0.1 M imidazole
PH range: 6.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2015 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.99→49.3 Å / Num. all: 182062 / Num. obs: 56584 / % possible obs: 99.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 87.43 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.053 / Net I/σ(I): 10.1 / Num. measured all: 182062 / Scaling rejects: 24
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.99-3.083.20.4682.61456345540.7680.31298
12.69-49.33.10.04920.523567640.9890.03498.2

-
Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
BUSTER-TNT1.10.0refinement
PDB_EXTRACT3.15data extraction
PHASER6.3.0phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZHX

4zhx


Resolution: 2.99→49.3 Å / Cor.coef. Fo:Fc: 0.9073 / Cor.coef. Fo:Fc free: 0.8933 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 4.496 / SU Rfree Blow DPI: 0.359
RfactorNum. reflection% reflectionSelection details
Rfree0.2452 2867 5.07 %RANDOM
Rwork0.2243 ---
obs0.2254 56562 99.3 %-
Displacement parametersBiso max: 175.46 Å2 / Biso mean: 68.78 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-2.016 Å20 Å2-3.0348 Å2
2---8.7512 Å20 Å2
3---6.7352 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: final / Resolution: 2.99→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14408 0 182 84 14674
Biso mean--59.39 46.94 -
Num. residues----1856
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4985SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes295HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2179HARMONIC5
X-RAY DIFFRACTIONt_it14989HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1979SEMIHARMONIC5
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_contact16268SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d14989HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg20434HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion1.54
X-RAY DIFFRACTIONt_other_torsion17.91
LS refinement shellResolution: 2.99→3.07 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2795 196 4.77 %
Rwork0.2731 3913 -
all0.2734 4109 -
obs--99.3 %
Refinement TLS params.Method: refined / Origin x: 119.3968 Å / Origin y: -35.0872 Å / Origin z: 35.6237 Å
111213212223313233
T0.406 Å2-0.0745 Å20.0325 Å2-0.3918 Å2-0.0152 Å2--0.392 Å2
L0.1111 °2-0.1907 °20.1086 °2-0.297 °2-0.1722 °2--0.0977 °2
S0.0061 Å °0.0191 Å °0.033 Å °0.0155 Å °0.0096 Å °0.025 Å °0.0165 Å °-0.054 Å °-0.0157 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ *|* }A8 - 545
2X-RAY DIFFRACTION1{ *|* }A8 - 545
3X-RAY DIFFRACTION1{ *|* }B78 - 270
4X-RAY DIFFRACTION1{ *|* }B78 - 270
5X-RAY DIFFRACTION1{ *|* }C9 - 545
6X-RAY DIFFRACTION1{ *|* }C9 - 545
7X-RAY DIFFRACTION1{ *|* }D77 - 269
8X-RAY DIFFRACTION1{ *|* }E24 - 326
9X-RAY DIFFRACTION1{ *|* }F25 - 324
10X-RAY DIFFRACTION1{ *|* }G5 - 8
11X-RAY DIFFRACTION1{ *|* }H1 - 85

+
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