[English] 日本語
Yorodumi
- PDB-4eai: Co-crystal structure of an AMPK core with AMP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4eai
TitleCo-crystal structure of an AMPK core with AMP
Components
  • 5'-AMP-activated protein kinase catalytic subunit alpha-1
  • 5'-AMP-activated protein kinase subunit beta-2
  • 5'-AMP-activated protein kinase subunit gamma-1
KeywordsTRANSFERASE / AMPK
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 ...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 / import into nucleus / positive regulation of fatty acid oxidation / positive regulation of skeletal muscle tissue development / CAMKK-AMPK signaling cascade / regulation of vesicle-mediated transport / cellular response to organonitrogen compound / protein kinase regulator activity / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of TOR signaling / negative regulation of hepatocyte apoptotic process / Carnitine metabolism / tau-protein kinase / bile acid and bile salt transport / nucleotide-activated protein kinase complex / cellular response to ethanol / protein localization to lipid droplet / bile acid signaling pathway / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / response to caffeine / motor behavior / positive regulation of protein targeting to mitochondrion / lipid biosynthetic process / negative regulation of tubulin deacetylation / Macroautophagy / AMP-activated protein kinase activity / positive regulation of protein localization / tau-protein kinase activity / cholesterol biosynthetic process / AMP binding / fatty acid oxidation / cellular response to nutrient levels / fatty acid homeostasis / cellular response to glucose starvation / Activation of AMPK downstream of NMDARs / negative regulation of lipid catabolic process / regulation of microtubule cytoskeleton organization / positive regulation of autophagy / energy homeostasis / response to UV / positive regulation of gluconeogenesis / negative regulation of insulin receptor signaling pathway / negative regulation of TORC1 signaling / positive regulation of adipose tissue development / cellular response to calcium ion / positive regulation of glycolytic process / response to activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / ADP binding / cellular response to glucose stimulus / response to gamma radiation / TP53 Regulates Metabolic Genes / positive regulation of glucose import / response to hydrogen peroxide / regulation of circadian rhythm / cellular response to hydrogen peroxide / Wnt signaling pathway / autophagy / neuron cellular homeostasis / cellular response to prostaglandin E stimulus / response to estrogen / fatty acid biosynthetic process / glucose metabolic process / rhythmic process / cellular response to xenobiotic stimulus / glucose homeostasis / cellular response to oxidative stress / positive regulation of cold-induced thermogenesis / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / nuclear speck / response to xenobiotic stimulus / apical plasma membrane / axon / negative regulation of gene expression / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / 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 / 5'-AMP-activated protein kinase beta subunit, interation domain / AMPK, C-terminal adenylate sensor 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 / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / 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 / 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: 2.285 Å
AuthorsChen, L. / Wang, J. / Zhang, Y.-Y. / Yan, S.F. / Neumann, D. / Schlattner, U. / Wang, Z.-X. / Wu, J.-W.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: AMP-activated protein kinase undergoes nucleotide-dependent conformational changes
Authors: Chen, L. / Wang, J. / Zhang, Y.-Y. / Yan, S.F. / Neumann, D. / Schlattner, U. / Wang, Z.-X. / Wu, J.-W.
History
DepositionMar 22, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref_seq_dif
Item: _entity.details / _entity.pdbx_description ..._entity.details / _entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 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 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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-2
C: 5'-AMP-activated protein kinase subunit gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4606
Polymers59,4193
Non-polymers1,0423
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-38 kcal/mol
Surface area21190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.594, 115.334, 48.522
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
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: 12097.888 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Chimera protein of residues 405-479 and residues 540-559 from 5'-AMP-activated protein kinase catalytic subunit alpha-1 (Uniprot P54645), linked by linker GGGGGG
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prkaa1, Ampk1 / Production host: Escherichia coli (E. coli)
References: UniProt: P54645, non-specific serine/threonine protein kinase, [acetyl-CoA carboxylase] kinase, [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase, tau-protein kinase
#2: Protein 5'-AMP-activated protein kinase subunit beta-2 / AMPK subunit beta-2


Mass: 9886.648 Da / Num. of mol.: 1 / Fragment: UNP residues 189-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAB2 / Production host: Escherichia coli (E. coli) / References: UniProt: O43741
#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
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.26
Details: MES, 16% IPP, 1% 1,4-butanediol, pH 6.26, VAPOR DIFFUSION, HANGING DROP, temperature 298 K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.99583 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99583 Å / Relative weight: 1
ReflectionResolution: 2.285→30 Å / Num. all: 25462 / Num. obs: 24647 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 34.29 Å2
Reflection shellResolution: 2.285→2.34 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.23 / % possible all: 91.5

-
Processing

Software
NameVersionClassificationNB
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V8Q

2v8q


Resolution: 2.285→29.547 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8247 / SU ML: 0.31 / σ(F): 0.06 / Phase error: 24.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1172 5.06 %random
Rwork0.194 ---
all0.1969 25462 --
obs0.1969 23163 90.57 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.799 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso max: 173.9 Å2 / Biso mean: 46.9494 Å2 / Biso min: 11.38 Å2
Baniso -1Baniso -2Baniso -3
1-9.3533 Å2-0 Å2-0 Å2
2---2.0753 Å20 Å2
3----7.278 Å2
Refinement stepCycle: LAST / Resolution: 2.285→29.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3544 0 69 102 3715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043694
X-RAY DIFFRACTIONf_angle_d0.9085017
X-RAY DIFFRACTIONf_chiral_restr0.055591
X-RAY DIFFRACTIONf_plane_restr0.004604
X-RAY DIFFRACTIONf_dihedral_angle_d17.1811341
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2849-2.38890.30381340.24852273240777
2.3889-2.51480.27631250.2262567269285
2.5148-2.67220.27181460.21062658280490
2.6722-2.87840.28121570.20472783294092
2.8784-3.16770.25971560.19672813296994
3.1677-3.62540.27221480.1872925307396
3.6254-4.56490.19521520.16092952310496
4.5649-29.54980.24981540.19463020317494
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)
11.71520.12110.85111.1019-0.0871.03850.0046-0.09760.19170.21970.06750.319-0.5542-0.27120.13660.0844-0.1653-0.1837-0.0295-0.12080.14583.880939.2871-13.5484
20.03480.3104-0.15263.0236-1.90251.81960.344-0.0350.47780.0073-0.3405-0.1823-0.02010.4830.04040.026-0.00660.00280.11970.05790.42110.641928.7851-18.6338
31.9826-2.52410.41435.499-0.61390.7847-0.20840.2776-0.0620.4091-0.01240.1292-0.12270.04250.22550.1288-0.019-0.05450.13040.0130.23970.387536.4146-20.9768
42.14422.09850.33772.08810.11960.7819-0.09690.0112-0.32170.0903-0.0414-0.55820.0501-0.02430.05780.09870.0199-0.04260.0983-0.02750.16072.045726.6322-11.7315
54.64633.63530.95063.72230.67250.59610.0434-0.09520.6105-0.4926-0.34260.36590.04730.04080.33080.3328-0.0772-0.12510.35390.07930.5176-3.588944.0105-27.2138
62.33071.26081.07392.4631-1.32382.52880.2023-0.02250.59850.0785-0.05820.51710.43940.2028-0.12670.26910.0519-0.07290.1350.03040.3359-13.331334.7628-22.6496
70.29590.39451.00242.2870.55583.8055-0.12220.0336-0.0032-0.0193-0.08-0.3933-0.15510.38980.1550.0755-0.03920.02020.11370.00480.1392-7.436430.5676-19.0715
80.1551-0.04780.2790.0149-0.08330.49750.2534-0.09650.2133-0.2561-0.18030.09450.05370.0199-0.08150.48970.0104-0.00240.3192-0.14920.3307-9.84730.4925-2.3433
90.36530.09370.11380.4518-0.27510.2611-0.130.0410.0335-0.1216-0.1427-0.0216-0.05560.11040.19140.13-0.00870.02260.1507-0.03020.0796-7.120421.0839-19.4253
100.23520.06760.14050.2804-0.24830.3507-0.0406-0.0555-0.00630.0645-0.0502-0.0075-0.0515-0.06140.04880.09160.036-0.01690.1021-0.02090.0769-12.782510.8941-8.1631
110.5643-0.5907-0.36651.39980.68530.35610.4063-0.1031-0.0123-0.3879-0.42470.121-0.0908-0.54420.00630.358-0.1126-0.02230.3302-0.03310.0575-8.851111.94555.2964
121.18960.67770.14740.44550.45420.5771-0.0083-0.0416-0.0504-0.00930.0365-0.0920.3139-0.0974-0.02130.18760.0068-0.0250.0751-0.00670.0737-18.5743-1.3887-16.4731
130.48210.38420.65170.64790.92341.8423-0.1876-0.41130.0215-0.039-0.26320.033-0.022-0.59550.37080.12220.0595-0.07570.3068-0.16010.1336-32.84925.3928-2.7993
140.76410.01730.05540.69130.14041.21610.29560.2696-0.07910.51410.4116-0.0906-0.2051-0.0691-0.63281.0736-0.059-0.23190.7381-0.03670.5313-36.78612.5655-12.0587
150.98580.5873-0.15751.02530.33820.39620.13520.1023-0.0076-0.1245-0.2102-0.01260.154-0.19240.0540.1794-0.0707-0.02750.1802-0.030.1154-30.6575-5.8549-17.9458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 394:425)A394 - 425
2X-RAY DIFFRACTION2(chain A and resid 426:445)A426 - 445
3X-RAY DIFFRACTION3(chain A and resid 446:472)A446 - 472
4X-RAY DIFFRACTION4(chain A and resid 473:493)A473 - 493
5X-RAY DIFFRACTION5(chain B and resid 204:210)B204 - 210
6X-RAY DIFFRACTION6(chain B and resid 211:236)B211 - 236
7X-RAY DIFFRACTION7(chain B and resid 237:245)B237 - 245
8X-RAY DIFFRACTION8(chain B and resid 246:251)B246 - 251
9X-RAY DIFFRACTION9(chain B and resid 252:271)B252 - 271
10X-RAY DIFFRACTION10(chain C and resid 26:106)C26 - 106
11X-RAY DIFFRACTION11(chain C and resid 107:126)C107 - 126
12X-RAY DIFFRACTION12(chain C and resid 127:222)C127 - 222
13X-RAY DIFFRACTION13(chain C and resid 223:265)C223 - 265
14X-RAY DIFFRACTION14(chain C and resid 266:273)C266 - 273
15X-RAY DIFFRACTION15(chain C and resid 274:324)C274 - 324

+
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