[English] 日本語
Yorodumi
- PDB-4red: Crystal structure of human AMPK alpha1 KD-AID with K43A mutation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4red
TitleCrystal structure of human AMPK alpha1 KD-AID with K43A mutation
Components5'-AMP-activated protein kinase catalytic subunit alpha-1
KeywordsTRANSFERASE / Kinase Domain Fold / phosphorylate numerous cellular targets / upregulate ATP-generating pathways upon activation / AMPK beta and gamma subunits
Function / homology
Function and homology information


negative regulation of glucosylceramide biosynthetic process / positive regulation of mitochondrial transcription / [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 ...negative regulation of glucosylceramide biosynthetic process / positive regulation of mitochondrial transcription / [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 / regulation of bile acid secretion / positive regulation of skeletal muscle tissue development / CAMKK-AMPK signaling cascade / regulation of vesicle-mediated transport / positive regulation of cholesterol biosynthetic process / cellular response to organonitrogen compound / 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 / response to caffeine / motor behavior / positive regulation of protein targeting to mitochondrion / lipid biosynthetic 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 / 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 / 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 / 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 / cellular response to hypoxia / 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 / chromatin / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / signal transduction / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
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 / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / KA1 domain/Ssp2, C-terminal / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...PRKAA1, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase alpha 1 catalytic subunit, C-terminal / : / AMP-activated protein kinase, alpha subunit, autoinhibitory domain / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / KA1 domain/Ssp2, C-terminal / 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. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
5'-AMP-activated protein kinase catalytic subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsZhou, X.E. / Ke, J. / Li, X. / Wang, L. / Gu, X. / de Waal, P.W. / Tan, M.H.E. / Wang, D. / Wu, D. / Xu, H.E. / Melcher, K.
CitationJournal: Cell Res. / Year: 2015
Title: Structural basis of AMPK regulation by adenine nucleotides and glycogen.
Authors: Li, X. / Wang, L. / Zhou, X.E. / Ke, J. / de Waal, P.W. / Gu, X. / Tan, M.H. / Wang, D. / Wu, D. / Xu, H.E. / Melcher, K.
History
DepositionSep 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Mar 11, 2015Group: Structure summary
Revision 1.3Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
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 catalytic subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)80,4002
Polymers80,4002
Non-polymers00
Water54030
1
A: 5'-AMP-activated protein kinase catalytic subunit alpha-1
B: 5'-AMP-activated protein kinase catalytic subunit alpha-1

A: 5'-AMP-activated protein kinase catalytic subunit alpha-1
B: 5'-AMP-activated protein kinase catalytic subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)160,8014
Polymers160,8014
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_455-x-1,-y,z1
Buried area17360 Å2
ΔGint-94 kcal/mol
Surface area58040 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-25 kcal/mol
Surface area33260 Å2
MethodPISA
3
A: 5'-AMP-activated protein kinase catalytic subunit alpha-1

B: 5'-AMP-activated protein kinase catalytic subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)80,4002
Polymers80,4002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_455-x-1,-y,z1
Buried area3700 Å2
ΔGint-20 kcal/mol
Surface area34000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.532, 119.532, 215.639
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.221744, -0.975105, 0.000106), (-0.975101, 0.221743, 0.002865), (-0.002818, 0.000532, -0.999996)-72.72817, -58.13783, 11.14912

-
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: 40200.234 Da / Num. of mol.: 2 / Fragment: human AMPK KD-AID, UNP residues 22-362 / Mutation: K43A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMPK Alpha1 (11-353), AMPK1, PRKAA1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q13131, non-specific serine/threonine protein kinase, [acetyl-CoA carboxylase] kinase, [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase, tau-protein kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.4 Å3/Da / Density % sol: 48.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.5 M HNa2PO4/0.5 M HK2PO4, 0.1 M Tris hydrochloride, pH 8.5, 0.1 M H(NH4)2PO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07806 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 13, 2012
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07806 Å / Relative weight: 1
ReflectionResolution: 2.95→30 Å / Num. all: 16876 / Num. obs: 16876 / % possible obs: 100 % / Redundancy: 17.3 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 32.3
Reflection shellResolution: 2.95→3.06 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H6D

2h6d


Resolution: 2.95→29.9 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.897 / SU B: 19.358 / SU ML: 0.363 / Cross valid method: THROUGHOUT / ESU R Free: 0.489 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27681 1222 7.3 %RANDOM
Rwork0.2297 ---
obs0.23312 15630 99.75 %-
all-15669 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.763 Å2
Baniso -1Baniso -2Baniso -3
1--2.01 Å20 Å2-0 Å2
2---2.01 Å20 Å2
3---4.03 Å2
Refinement stepCycle: LAST / Resolution: 2.95→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5293 0 0 30 5323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195412
X-RAY DIFFRACTIONr_bond_other_d0.0110.025212
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9697315
X-RAY DIFFRACTIONr_angle_other_deg0.89312027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7995654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60423.92250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.65415971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0841532
X-RAY DIFFRACTIONr_chiral_restr0.0690.2806
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216006
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021218
X-RAY DIFFRACTIONr_mcbond_it4.7877.1292631
X-RAY DIFFRACTIONr_mcbond_other4.7877.1292630
X-RAY DIFFRACTIONr_mcangle_it7.38410.6883280
X-RAY DIFFRACTIONr_mcangle_other7.38310.6883281
X-RAY DIFFRACTIONr_scbond_it4.8637.5482778
X-RAY DIFFRACTIONr_scbond_other4.8567.5482778
X-RAY DIFFRACTIONr_scangle_other7.38611.1854035
X-RAY DIFFRACTIONr_long_range_B_refined12.42666.79421526
X-RAY DIFFRACTIONr_long_range_B_other12.42566.79421526
LS refinement shellResolution: 2.949→3.025 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 86 -
Rwork0.288 1122 -
obs--99.42 %

+
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