[English] 日本語
Yorodumi
- PDB-2v8q: Crystal structure of the regulatory fragment of mammalian AMPK in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2v8q
TitleCrystal structure of the regulatory fragment of mammalian AMPK in complexes 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 / PHOSPHORYLATION / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE / KINASE / MAGNESIUM / CBS DOMAIN
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 / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / positive regulation of mitochondrial transcription / AMPK inhibits chREBP transcriptional activation activity ...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 / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / positive regulation of mitochondrial transcription / AMPK inhibits chREBP transcriptional activation activity / histone H2BS36 kinase activity / cold acclimation / AMP-activated protein kinase 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 / negative regulation of hepatocyte apoptotic process / positive regulation of fatty acid oxidation / Energy dependent regulation of mTOR by LKB1-AMPK / Carnitine shuttle / positive regulation of T cell mediated immune response to tumor cell / tau-protein kinase / protein kinase regulator activity / negative regulation of TOR signaling / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / response to caffeine / positive regulation of protein targeting to mitochondrion / regulation of glycolytic process / protein localization to lipid droplet / negative regulation of tubulin deacetylation / AMP binding / cellular response to stress / Macroautophagy / cholesterol biosynthetic process / lipid biosynthetic process / fatty acid oxidation / motor behavior / cellular response to ethanol / fatty acid homeostasis / negative regulation of lipid catabolic process / cellular response to nutrient levels / response to UV / cellular response to glucose starvation / energy homeostasis / Activation of AMPK downstream of NMDARs / positive regulation of protein localization / negative regulation of TORC1 signaling / positive regulation of adipose tissue development / positive regulation of gluconeogenesis / positive regulation of autophagy / negative regulation of insulin receptor signaling pathway / cellular response to calcium ion / regulation of microtubule cytoskeleton organization / positive regulation of glycolytic process / response to activity / response to gamma radiation / positive regulation of D-glucose import / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cellular response to glucose stimulus / response to hydrogen peroxide / regulation of circadian rhythm / neuron cellular homeostasis / ADP binding / positive regulation of T cell activation / autophagy / response to estrogen / cellular response to xenobiotic stimulus / Wnt signaling pathway / cellular response to hydrogen peroxide / glucose metabolic process / fatty acid biosynthetic process / rhythmic process / glucose homeostasis / cellular response to prostaglandin E stimulus / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / negative regulation of translation / nuclear speck / ciliary basal body / apical plasma membrane / response to xenobiotic stimulus / axon / negative regulation of gene expression / protein serine kinase activity / neuronal cell body / protein serine/threonine kinase activity / positive regulation of cell population proliferation / dendrite / chromatin binding
Similarity search - Function
Double Stranded RNA Binding Domain - #60 / Double Stranded RNA Binding 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 ...Double Stranded RNA Binding Domain - #60 / Double Stranded RNA Binding 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 / Other non-globular / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Special / 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsXiao, B. / Heath, R. / Saiu, P. / Leiper, F.C. / Leone, P. / Jing, C. / Walker, P.A. / Haire, L. / Eccleston, J.F. / Davis, C.T. ...Xiao, B. / Heath, R. / Saiu, P. / Leiper, F.C. / Leone, P. / Jing, C. / Walker, P.A. / Haire, L. / Eccleston, J.F. / Davis, C.T. / Martin, S.R. / Carling, D. / Gamblin, S.J.
CitationJournal: Nature / Year: 2007
Title: Structural Basis for AMP Binding to Mammalian AMP-Activated Protein Kinase
Authors: Xiao, B. / Heath, R. / Saiu, P. / Leiper, F.C. / Leone, P. / Jing, C. / Walker, P.A. / Haire, L. / Eccleston, J.F. / Davis, C.T. / Martin, S.R. / Carling, D. / Gamblin, S.J.
History
DepositionAug 13, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
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
E: 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1526
Polymers65,1113
Non-polymers1,0423
Water7,710428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-49 kcal/mol
Surface area30320 Å2
MethodPQS
Unit cell
Length a, b, c (Å)48.522, 119.390, 129.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein 5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-1 / AMP-ACTIVATED PROTEIN KINASE / AMPK ALPHA-1 CHAIN


Mass: 17635.799 Da / Num. of mol.: 1 / Fragment: RESIDUES 396-548
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P54645, non-specific serine/threonine protein kinase
#2: Protein 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT BETA-2 / AMP-ACTIVATED PROTEIN KINASE / AMPK BETA-2 CHAIN


Mass: 10040.813 Da / Num. of mol.: 1 / Fragment: RESIDUES 187-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O43741
#3: Protein 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1 / AMP-ACTIVATED PROTEIN KINASE / AMPK GAMMA-1 CHAIN / AMPKG


Mass: 37434.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P80385
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST FOUR RESIDUES (GSMA) OF THE SEQUENCE OF CHAIN A ARE GENERATED FROM THE POST HIS-TAG ...THE FIRST FOUR RESIDUES (GSMA) OF THE SEQUENCE OF CHAIN A ARE GENERATED FROM THE POST HIS-TAG CLEAVAGE THE FIRST RESIDUES (M) OF THE SEQUENCE OF CHAIN B IS GENERATED BY THE WAY IT WAS CLONED INTO THE VECTOR

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 42012 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.7

-
Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.937 / SU B: 10.644 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2234 5 %RANDOM
Rwork0.212 ---
obs0.213 42012 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.84 Å2
Baniso -1Baniso -2Baniso -3
1--2.73 Å20 Å20 Å2
2--3.06 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3884 0 69 428 4381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224044
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.9855491
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4755474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23323.314172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.37915718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9411525
X-RAY DIFFRACTIONr_chiral_restr0.110.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022935
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.21867
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22708
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2364
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6821.52452
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.15723919
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.43531803
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2334.51572
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.21 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.298 308
Rwork0.263 5903
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)
11.5999-0.68120.78863.3406-1.47495.218-0.06770.07310.0023-0.1302-0.1409-0.0138-0.1520.45080.20860.0278-0.0765-0.017-0.17730.028-0.096219.70173.30511.257
21.4078-1.53721.04233.0635-3.61735.2095-0.1041-0.26740.05940.27660.032-0.0624-0.6652-0.31980.07210.18170.002-0.0246-0.1799-0.0207-0.041813.74377.13218.173
33.8083-0.57182.24130.4347-0.24421.34360.03450.2486-0.0285-0.0464-0.1273-0.15260.0530.34670.09280.03580.00860.0515-0.00190.1520.016635.68257.68631.437
41.09230.3548-0.42031.7073-1.42892.7792-0.0389-0.0185-0.0918-0.22440.18910.15680.3833-0.1929-0.15020.0654-0.0436-0.0308-0.1480.07270.004511.2247.90335.042
52.6590.48060.45752.57870.16862.18850.0639-0.2307-0.07840.0459-0.00490.10870.1142-0.0525-0.0590.03470.03290.0232-0.15170.078-0.037616.60842.74154.413
63.64310.35340.59071.8763-0.22044.54180.1641-0.16410.51410.1617-0.104-0.0889-0.44990.2731-0.06020.0464-0.03210.0514-0.12250.01390.060232.38457.02951.822
70.0981-0.20260.25980.4695-0.40261.0409-0.04410.0103-0.0022-0.07090.02960.00080.0717-0.00230.01440.0312-0.01350.0119-0.12490.0499-0.002420.70758.35232.538
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A393 - 469
2X-RAY DIFFRACTION1A524 - 548
3X-RAY DIFFRACTION2B190 - 222
4X-RAY DIFFRACTION2B233 - 272
5X-RAY DIFFRACTION3E48 - 128
6X-RAY DIFFRACTION4E23 - 47
7X-RAY DIFFRACTION4E129 - 183
8X-RAY DIFFRACTION5E184 - 203
9X-RAY DIFFRACTION5E275 - 326
10X-RAY DIFFRACTION6E204 - 274
11X-RAY DIFFRACTION6E1327 - 1329
12X-RAY DIFFRACTION7A - E2001 - 2291

+
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