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- EMDB-36216: local map of hPhK alpha-gamma subcomplex in active state -

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Basic information

Entry
Database: EMDB / ID: EMD-36216
Titlelocal map of hPhK alpha-gamma subcomplex in active state
Map data
Sample
  • Complex: local map of hPhK alpha-gamma subcomplex
Keywordslocal map of hPhK alpha-gamma subcomplex / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


phosphorylase kinase / phosphorylase kinase activity / phosphorylase kinase complex / positive regulation of glycogen catabolic process / tau-protein kinase / Glycogen breakdown (glycogenolysis) / glycogen metabolic process / generation of precursor metabolites and energy / carbohydrate metabolic process / calmodulin binding ...phosphorylase kinase / phosphorylase kinase activity / phosphorylase kinase complex / positive regulation of glycogen catabolic process / tau-protein kinase / Glycogen breakdown (glycogenolysis) / glycogen metabolic process / generation of precursor metabolites and energy / carbohydrate metabolic process / calmodulin binding / non-specific serine/threonine protein kinase / protein serine kinase activity / enzyme binding / signal transduction / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Phosphorylase kinase alpha/beta subunit / Phosphorylase b kinase regulatory subunit alpha/beta, C-terminal domain / Phosphorylase b kinase C-terminal domain / Phosphorylase kinase, gamma catalytic subunit / GH15-like domain / Glycosyl hydrolases family 15 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Phosphorylase kinase alpha/beta subunit / Phosphorylase b kinase regulatory subunit alpha/beta, C-terminal domain / Phosphorylase b kinase C-terminal domain / Phosphorylase kinase, gamma catalytic subunit / GH15-like domain / Glycosyl hydrolases family 15 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / 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
Phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform / Phosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsYang XK / Xiao JY
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2024
Title: Architecture and activation of human muscle phosphorylase kinase.
Authors: Xiaoke Yang / Mingqi Zhu / Xue Lu / Yuxin Wang / Junyu Xiao /
Abstract: The study of phosphorylase kinase (PhK)-regulated glycogen metabolism has contributed to the fundamental understanding of protein phosphorylation; however, the molecular mechanism of PhK remains ...The study of phosphorylase kinase (PhK)-regulated glycogen metabolism has contributed to the fundamental understanding of protein phosphorylation; however, the molecular mechanism of PhK remains poorly understood. Here we present the high-resolution cryo-electron microscopy structures of human muscle PhK. The 1.3-megadalton PhK αβγδ hexadecamer consists of a tetramer of tetramer, wherein four αβγδ modules are connected by the central β scaffold. The α- and β-subunits possess glucoamylase-like domains, but exhibit no detectable enzyme activities. The α-subunit serves as a bridge between the β-subunit and the γδ subcomplex, and facilitates the γ-subunit to adopt an autoinhibited state. Ca-free calmodulin (δ-subunit) binds to the γ-subunit in a compact conformation. Upon binding of Ca, a conformational change occurs, allowing for the de-inhibition of the γ-subunit through a spring-loaded mechanism. We also reveal an ADP-binding pocket in the β-subunit, which plays a role in allosterically enhancing PhK activity. These results provide molecular insights of this important kinase complex.
History
DepositionMay 18, 2023-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBc / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_36216.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.24
Minimum - Maximum-2.680255 - 4.921381
Average (Standard dev.)-0.00060270954 (±0.04542719)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 481.50003 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : local map of hPhK alpha-gamma subcomplex

EntireName: local map of hPhK alpha-gamma subcomplex
Components
  • Complex: local map of hPhK alpha-gamma subcomplex

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Supramolecule #1: local map of hPhK alpha-gamma subcomplex

SupramoleculeName: local map of hPhK alpha-gamma subcomplex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: OTHER / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 432047
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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