[English] 日本語
Yorodumi
- PDB-6c9h: non-phosphorylated AMP-activated protein kinase bound to pharmaco... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6c9h
Titlenon-phosphorylated AMP-activated protein kinase bound to pharmacological activator R734
Components
  • (5'-AMP-activated protein kinase subunit ...) x 2
  • 5'-AMP-activated protein kinase catalytic subunit alpha-1
KeywordsTRANSFERASE / AMPK / activator / R734
Function / homology
Function and homology information


negative regulation of glucosylceramide biosynthetic process / positive regulation of mitochondrial transcription / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / : / regulation of stress granule assembly / histone H2BS36 kinase activity / regulation of peptidyl-serine phosphorylation / cold acclimation ...negative regulation of glucosylceramide biosynthetic process / positive regulation of mitochondrial transcription / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / : / regulation of stress granule assembly / histone H2BS36 kinase 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 skeletal muscle tissue development / CAMKK-AMPK signaling cascade / cAMP-dependent protein kinase regulator activity / regulation of vesicle-mediated transport / positive regulation of cholesterol biosynthetic process / 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 / 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 / regulation of glycolytic process / cAMP-dependent protein kinase activity / 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 / positive regulation of protein kinase activity / 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 / 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 / tau protein binding / 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 / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / nuclear speck / apical plasma membrane / axon / negative regulation of gene expression / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / neuronal cell body / chromatin binding / positive regulation of cell population proliferation
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 / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase ...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 / 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
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Chem-R34 / STAUROSPORINE / 5'-AMP-activated protein kinase subunit gamma-1 / 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: 2.65 Å
AuthorsYan, Y. / Zhou, X.E. / Novick, S. / Shaw, S.J. / Li, Y. / Hitoshi, Y. / Brunzelle, J.S. / Griffin, P.R. / Xu, H.E. / Melcher, K.
Funding support United States, China, 8items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM102545 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)DK071662 United States
National Natural Science Foundation of China (NSFC)31300245 China
Ministry of Science and Technology (MoST, China)2012ZX09301001 China
Ministry of Science and Technology (MoST, China)2012CB910403 China
Ministry of Science and Technology (MoST, China)2013CB910600 China
Ministry of Science and Technology (MoST, China)XDB08020303 China
Ministry of Science and Technology (MoST, China)2013ZX09507001 China
CitationJournal: J. Biol. Chem. / Year: 2019
Title: Structures of AMP-activated protein kinase bound to novel pharmacological activators in phosphorylated, non-phosphorylated, and nucleotide-free states.
Authors: Yan, Y. / Zhou, X.E. / Novick, S.J. / Shaw, S.J. / Li, Y. / Brunzelle, J.S. / Hitoshi, Y. / Griffin, P.R. / Xu, H.E. / Melcher, K.
History
DepositionJan 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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)119,8188
Polymers117,8633
Non-polymers1,9555
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15840 Å2
ΔGint-81 kcal/mol
Surface area41160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.016, 124.016, 404.180
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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: 57165.641 Da / Num. of mol.: 1 / Mutation: S108D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAA1, AMPK1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13131, non-specific serine/threonine protein kinase, [acetyl-CoA carboxylase] kinase, [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase, tau-protein kinase

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

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


Mass: 23071.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAB1, AMPK / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y478
#3: Protein 5'-AMP-activated protein kinase subunit gamma-1 / AMPKg


Mass: 37626.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAG1 / Production host: Escherichia coli (E. coli) / References: UniProt: P54619

-
Non-polymers , 4 types, 85 molecules

#4: Chemical ChemComp-R34 / 5-{[6-chloro-5-(1-methyl-1H-indol-5-yl)-1H-benzimidazol-2-yl]oxy}-N-hydroxy-2-methylbenzamide


Mass: 446.886 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H19ClN4O3
#5: Chemical ChemComp-STU / STAUROSPORINE / Staurosporine


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


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


Mass: 18.015 Da / Num. of mol.: 80 / 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: 3.81 Å3/Da / Density % sol: 67.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2 M magnesium formate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0782 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0782 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 54649 / % possible obs: 99.7 % / Redundancy: 33.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.571 / Net I/σ(I): 12.1
Reflection shellResolution: 2.65→2.73 Å / Rmerge(I) obs: 0.716 / Num. unique obs: 4387 / CC1/2: 0.72

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RER

4rer


Resolution: 2.65→49.884 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2423 3678 7.24 %
Rwork0.2133 --
obs0.2154 50807 93.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→49.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7285 0 136 80 7501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037610
X-RAY DIFFRACTIONf_angle_d0.75810344
X-RAY DIFFRACTIONf_dihedral_angle_d8.2714542
X-RAY DIFFRACTIONf_chiral_restr0.0431164
X-RAY DIFFRACTIONf_plane_restr0.0051283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6501-2.6850.3297740.2856974X-RAY DIFFRACTION51
2.685-2.72180.3007830.29741071X-RAY DIFFRACTION57
2.7218-2.76060.30181020.30021168X-RAY DIFFRACTION61
2.7606-2.80180.33631030.27651334X-RAY DIFFRACTION71
2.8018-2.84560.31071150.28111555X-RAY DIFFRACTION82
2.8456-2.89230.30581420.27881917X-RAY DIFFRACTION100
2.8923-2.94210.33941510.27541912X-RAY DIFFRACTION100
2.9421-2.99560.28021680.27091864X-RAY DIFFRACTION100
2.9956-3.05320.32251530.26881901X-RAY DIFFRACTION100
3.0532-3.11550.29121550.26571922X-RAY DIFFRACTION100
3.1155-3.18330.29421430.26211935X-RAY DIFFRACTION100
3.1833-3.25730.27181440.26871920X-RAY DIFFRACTION100
3.2573-3.33880.29291450.26431913X-RAY DIFFRACTION100
3.3388-3.4290.29851420.23371924X-RAY DIFFRACTION100
3.429-3.52990.24971420.22811942X-RAY DIFFRACTION100
3.5299-3.64380.2421490.21971948X-RAY DIFFRACTION100
3.6438-3.7740.25391730.21941903X-RAY DIFFRACTION100
3.774-3.9250.25111380.19851938X-RAY DIFFRACTION100
3.925-4.10360.20791490.18721960X-RAY DIFFRACTION100
4.1036-4.31980.23781630.17741942X-RAY DIFFRACTION100
4.3198-4.59030.19441630.16541956X-RAY DIFFRACTION100
4.5903-4.94440.19571490.17461973X-RAY DIFFRACTION100
4.9444-5.44140.20671400.18661998X-RAY DIFFRACTION100
5.4414-6.22760.18851540.20512022X-RAY DIFFRACTION100
6.2276-7.84110.27621650.21812047X-RAY DIFFRACTION100
7.8411-49.89280.20051730.18432190X-RAY DIFFRACTION100
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)
10.00070.01240.01150.06280.02110.0444-0.03790.02760.01650.03410.0797-0.003-0.19330.04260.10910.1878-0.0267-0.0197-0.1412-0.3231-0.184-26.581725.2783-16.4065
20.001-0.0017-0.00080.00160.00090.001-0.0052-0.00840.028-0.0039-0.00730.0230.0008-0.0146-00.43570.0134-0.00740.4089-0.05680.4006-18.536840.6222-0.625
30.0004-0.0006-00.002-0.0010.001-0.0019-0.01040.01060.0233-0.00070.0158-0.0153-0.018900.88920.03670.02290.8776-0.01470.914-24.697143.633611.1107
40.0139-0.00230.00010.00720.00620.00850.08080.0257-0.045-0.0585-0.0250.0712-0.0537-0.0007-00.70660.2747-0.16580.4848-0.14590.5815-53.649451.2507-14.1175
50.06180.05890.01090.07360.00770.00560.0427-0.04390.06750.0638-0.00450.0232-0.0504-0.0270.02920.2892-0.0927-0.00160.2203-0.10.1757-13.250535.4893-49.6937
60.0125-0.01180.00950.01570.0070.01350.0104-0.0056-0.0099-0.0532-0.0087-0.01020.0006-0.01280.00130.45130.28940.00850.3891-0.16060.4662-46.453347.6867-3.209
70.0019-0.0009-0.00220.00070.00380.0019-0.00680.0026-0.0001-0.0164-0.0284-0.01820.00080.030100.4810.06710.06520.6051-0.18410.555-26.245359.36324.9853
80.0027-0.0051-0.00040.0058-0.00120.0005-0.0106-0.00310.0024-0.0827-0.0237-0.0091-0.037-0.019-0.00730.38860.19960.00220.2878-0.12970.4405-54.334869.00258.0863
90.00420.00110.00080.00510.00370.00350.0038-0.01040.0537-0.02850.0331-0.0481-0.04240.0615-00.5070.02290.15470.5769-0.140.642-29.087866.25669.2948
100.0014-0.0007-00.00310.00270.00060.0107-0.01810.00160.01910.0116-0.0408-0.03130.0171-00.29190.0932-0.01930.3244-0.11540.3877-42.33672.707329.6987
110.0044-0.004-0.00050.01150.010.00810.0186-0.0418-0.00540.04710.0261-0.0283-0.02550.057600.32730.1788-0.01540.5492-0.10680.588-38.127762.94226.6065
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 276 )
2X-RAY DIFFRACTION2chain 'A' and (resid 277 through 320 )
3X-RAY DIFFRACTION3chain 'A' and (resid 321 through 362 )
4X-RAY DIFFRACTION4chain 'A' and (resid 363 through 549 )
5X-RAY DIFFRACTION5chain 'B' and (resid 74 through 170 )
6X-RAY DIFFRACTION6chain 'B' and (resid 171 through 270 )
7X-RAY DIFFRACTION7chain 'C' and (resid 26 through 48 )
8X-RAY DIFFRACTION8chain 'C' and (resid 49 through 120 )
9X-RAY DIFFRACTION9chain 'C' and (resid 121 through 195 )
10X-RAY DIFFRACTION10chain 'C' and (resid 196 through 235 )
11X-RAY DIFFRACTION11chain 'C' and (resid 236 through 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