[English] 日本語
Yorodumi
- PDB-4eal: Co-crystal of AMPK core with ATP soaked with AMP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4eal
TitleCo-crystal of AMPK core with ATP soaked with AMP
Components
  • 5'-AMP-activated protein kinase catalytic subunit alpha-1
  • 5'-AMP-activated protein kinase subunit beta-1
  • 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 / Regulation of TP53 Activity through Phosphorylation / Macroautophagy / TP53 Regulates Metabolic Genes / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / positive regulation of mitochondrial transcription ...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 / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / positive regulation of mitochondrial transcription / negative regulation of tubulin deacetylation / histone H2BS36 kinase activity / cold acclimation / AMP-activated protein kinase activity / lipid droplet disassembly / phosphatidylethanolamine biosynthetic process / regulation of carbon utilization / positive regulation of skeletal muscle tissue development / CAMKK-AMPK signaling cascade / import into nucleus / phosphatidylcholine biosynthetic process / regulation of vesicle-mediated transport / nucleotide-activated protein kinase complex / negative regulation of T cell mediated immune response to tumor cell / protein localization to lysosome / negative regulation of hepatocyte apoptotic process / positive regulation of fatty acid oxidation / negative regulation of T cell activation / positive regulation of T cell mediated immune response to tumor cell / protein K6-linked ubiquitination / tau-protein kinase / regulation of vascular permeability / protein kinase regulator activity / negative regulation of TOR signaling / negative regulation of protein localization to nucleus / response to caffeine / regulation of glycolytic process / : / protein localization to lipid droplet / tau-protein kinase activity / lysosome organization / cellular response to stress / cholesterol biosynthetic process / lipid biosynthetic process / TORC1 signaling / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / AMP binding / hepatocyte apoptotic process / fatty acid oxidation / motor behavior / positive regulation of release of cytochrome c from mitochondria / positive regulation of translational initiation / cellular response to ethanol / fatty acid homeostasis / autophagosome assembly / negative regulation of lipid catabolic process / response to UV / cellular response to glucose starvation / energy homeostasis / positive regulation of protein localization / positive regulation of adipose tissue development / negative regulation of TORC1 signaling / cellular response to nutrient levels / negative regulation of translational initiation / positive regulation of autophagy / positive regulation of TORC1 signaling / negative regulation of insulin receptor signaling pathway / positive regulation of gluconeogenesis / cellular response to calcium ion / regulation of microtubule cytoskeleton organization / cellular response to amino acid starvation / positive regulation of glycolytic process / cellular response to starvation / response to activity / positive regulation of D-glucose import across plasma membrane / response to gamma radiation / protein localization to plasma membrane / circadian regulation of gene expression / response to hydrogen peroxide / cellular response to glucose stimulus / neuron cellular homeostasis / ADP binding / regulation of circadian rhythm / response to estrogen / autophagy / cellular response to xenobiotic stimulus / protein destabilization / glucose metabolic process / Wnt signaling pathway / cellular response to hydrogen peroxide / positive regulation of T cell activation / fatty acid biosynthetic process / glucose homeostasis / cellular response to prostaglandin E stimulus / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / protein-containing complex assembly / cellular response to hypoxia / proteasome-mediated ubiquitin-dependent protein catabolic process / cytoplasmic translation
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 / 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
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.506 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-1
C: 5'-AMP-activated protein kinase subunit gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3605
Polymers57,6663
Non-polymers6942
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-32 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.850, 40.503, 77.738
Angle α, β, γ (deg.)90.00, 105.53, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-306-

HOH

-
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, EC: 2.7.11.27, [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase, tau-protein kinase
#2: Protein 5'-AMP-activated protein kinase subunit beta-1 / AMPKb / 5'-AMP-activated protein kinase 40 kDa subunit


Mass: 8133.786 Da / Num. of mol.: 1 / Fragment: UNP residues 200-270
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
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 0.1M MES pH5.9, 18% IPP, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 18505 / Num. obs: 18431 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 58.77 Å2
Reflection shellResolution: 2.5→2.54 Å / % possible all: 99.4

-
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: 2.506→24.967 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7758 / SU ML: 0.4 / σ(F): 0.07 / Phase error: 28.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2774 884 4.97 %
Rwork0.2324 --
obs0.2347 17779 95.98 %
all-18505 -
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.154 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso max: 179.85 Å2 / Biso mean: 75.9218 Å2 / Biso min: 28.08 Å2
Baniso -1Baniso -2Baniso -3
1--1.8684 Å20 Å2-9.1271 Å2
2--1.1113 Å2-0 Å2
3---0.7571 Å2
Refinement stepCycle: LAST / Resolution: 2.506→24.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3389 0 46 58 3493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033505
X-RAY DIFFRACTIONf_angle_d0.7294754
X-RAY DIFFRACTIONf_chiral_restr0.046566
X-RAY DIFFRACTIONf_plane_restr0.002575
X-RAY DIFFRACTIONf_dihedral_angle_d16.5381280
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5061-2.66290.29971290.27232569269889
2.6629-2.86820.31751370.26472721285894
2.8682-3.15640.28611270.25372836296397
3.1564-3.61190.30771700.23832874304499
3.6119-4.54620.21941650.19972932309799
4.5462-24.9680.27761560.21882963311998
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)
11.2752-0.135-0.89250.8817-0.13421.256-0.33330.6355-0.7548-0.051-0.49020.2804-0.10531.15660.70690.4418-0.0252-0.23071.04720.31520.961426.3452394.3026-22.876
20.3168-0.03720.13560.0066-0.02520.0512-0.0179-0.2916-0.0066-0.13220.2242-0.0719-0.08740.2357-0.03020.6855-0.0294-0.27682.30581.03190.969340.8558399.6048-15.467
33.22260.45-1.53740.1616-0.14530.76030.1924-1.04781.3754-0.22380.2851-0.1134-0.11520.4884-0.10840.5251-0.2047-0.3731.5570.55771.270433.4782404.1052-11.2575
40.95760.8501-1.51112.3617-0.76512.82190.279-1.1524-0.0344-0.0328-0.42040.5463-0.42792.07980.09890.8852-0.3104-0.35791.6750.23980.995629.641401.7625-4.6297
52.38381.1413-1.3131.8289-1.24472.79410.5967-1.23810.06040.1731-0.548-0.044-0.40291.1325-0.07040.7738-0.1516-0.08941.1485-0.10990.691417.5158404.8183-2.2409
61.32880.36620.79960.9037-0.38742.46650.4353-0.8214-0.16910.5806-0.6414-0.2674-0.4977-0.54750.09320.5523-0.2734-0.18721.31380.46480.47925.7087395.1745-8.5839
70.8674-0.42620.66432.0818-1.09490.82850.52840.0705-0.28480.0605-1.5912-1.19240.37431.46771.00860.57740.06640.12121.41380.64990.830335.7616391.6132-21.0745
81.28141.9953-1.06713.0057-1.92652.06420.31-1.0398-0.20.6167-0.8822-0.8145-0.2271.04660.51420.3779-0.1246-0.13460.58670.16910.568919.2893400.9454-12.5462
90.0898-0.1697-0.02250.8154-0.83051.3024-0.39540.1214-0.2952-0.9248-1.4820.64770.6310.53550.63091.33850.59790.51221.1631.1180.736527.4021385.3287-13.9294
103.44440.11780.24030.93021.27671.7860.64050.4474-0.4842-0.62310.3854-0.0310.0470.1339-0.73420.69890.0275-0.05940.47850.16470.499918.1441395.7566-21.7937
110.68560.7590.03972.1772-1.67661.25510.0867-0.0093-0.0630.4446-0.3819-0.2792-0.47210.0580.12130.43640.14580.02210.41880.05350.307310.5421394.7141-16.745
120.6279-0.18020.2520.7244-0.95680.4863-0.0202-0.1031-0.0894-0.0197-0.1475-0.1437-0.1423-0.16870.12460.43010.07680.02940.2823-0.11590.2242-3.6642393.2004-18.4279
130.4309-0.1866-0.1587-0.0378-0.26490.23290.1307-0.06730.2111-0.2863-0.06460.2039-0.2657-0.02-0.02670.52560.0508-0.04490.2382-0.10740.3153-1.1739408.4439-22.1685
141.2574-0.0930.05371.04910.15431.52020.1012-0.25120.25550.2019-0.18360.0597-0.2219-0.10760.04030.33070.1060.03270.2712-0.1180.2794-6.5931399.9839-16.0998
150.40860.55340.93052.2634-1.39582.91090.2141-0.390.19220.29660.36460.8834-0.0225-1.516-0.24480.3915-0.0548-0.0980.9934-0.0690.5289-27.8748389.0327-24.0179
161.20130.4867-0.27491.4972-0.241.0166-0.12240.542-0.1103-0.00590.1036-0.1461-0.391-0.5297-0.00840.47150.2312-0.03060.6182-0.14760.4525-16.1058404.841-38.3903
170.96341.4686-1.44491.144-0.78212.7078-0.090.5783-0.6013-0.1544-0.0556-0.43270.0395-0.79490.06240.33320.0318-0.10310.6641-0.05040.6089-18.2448395.5077-38.7672
180.39260.0903-0.38430.5064-0.26670.803-0.16070.49990.2978-0.08270.1310.02070.0998-0.71330.01810.231-0.0059-0.04720.5543-0.12610.5101-22.8112390.8084-28.1721
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 396:403)A396 - 403
2X-RAY DIFFRACTION2(chain A and resid 404:408)A404 - 408
3X-RAY DIFFRACTION3(chain A and resid 409:417)A409 - 417
4X-RAY DIFFRACTION4(chain A and resid 418:431)A418 - 431
5X-RAY DIFFRACTION5(chain A and resid 432:443)A432 - 443
6X-RAY DIFFRACTION6(chain A and resid 444:453)A444 - 453
7X-RAY DIFFRACTION7(chain A and resid 454:461)A454 - 461
8X-RAY DIFFRACTION8(chain A and resid 462:548)A462 - 548
9X-RAY DIFFRACTION9(chain B and resid 202:235)B202 - 235
10X-RAY DIFFRACTION10(chain B and resid 236:246)B236 - 246
11X-RAY DIFFRACTION11(chain B and resid 247:270)B247 - 270
12X-RAY DIFFRACTION12(chain C and resid 23:68)C23 - 68
13X-RAY DIFFRACTION13(chain C and resid 69:107)C69 - 107
14X-RAY DIFFRACTION14(chain C and resid 108:179)C108 - 179
15X-RAY DIFFRACTION15(chain C and resid 180:207)C180 - 207
16X-RAY DIFFRACTION16(chain C and resid 208:252)C208 - 252
17X-RAY DIFFRACTION17(chain C and resid 253:287)C253 - 287
18X-RAY DIFFRACTION18(chain C and resid 288:324)C288 - 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