+Open data
-Basic information
Entry | Database: PDB / ID: 8jfl | ||||||
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Title | PhK holoenzyme in active state, muscle isoform | ||||||
Components |
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Keywords | CYTOSOLIC PROTEIN / glycogen phosphorylase b kinase / muscle isoform / Ca2+ active state | ||||||
Function / homology | Function and homology information phosphorylase kinase / phosphorylase kinase activity / phosphorylase kinase complex / tau-protein kinase / glycogen biosynthetic process / Glycogen breakdown (glycogenolysis) / tau-protein kinase activity / glycogen metabolic process / generation of precursor metabolites and energy / calmodulin binding ...phosphorylase kinase / phosphorylase kinase activity / phosphorylase kinase complex / tau-protein kinase / glycogen biosynthetic process / Glycogen breakdown (glycogenolysis) / tau-protein kinase activity / glycogen metabolic process / generation of precursor metabolites and energy / calmodulin binding / non-specific serine/threonine protein kinase / carbohydrate metabolic process / phosphorylation / protein serine kinase activity / enzyme binding / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Yang, X.K. / Xiao, J.Y. | ||||||
Funding support | China, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jfl.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8jfl.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 8jfl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/8jfl ftp://data.pdbj.org/pub/pdb/validation_reports/jf/8jfl | HTTPS FTP |
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-Related structure data
Related structure data | 36213MC 8jfkC 8xy7C 8xyaC 8xybC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 137469.422 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PHKA1, PHKA / Production host: Homo sapiens (human) / References: UniProt: P46020 #2: Protein | Mass: 45084.672 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PHKG1, PHKG / Production host: Homo sapiens (human) References: UniProt: Q16816, phosphorylase kinase, non-specific serine/threonine protein kinase, tau-protein kinase #3: Protein | Mass: 125032.961 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PHKB / Production host: Homo sapiens (human) / References: UniProt: Q93100 #4: Chemical | ChemComp-FAR / #5: Chemical | ChemComp-ADP / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: phosphorylase b kinase, muscle isoform, Ca2+ active state Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8.2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: OTHER / Nominal defocus max: 1500 nm / Nominal defocus min: 1100 nm |
Image recording | Electron dose: 1.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 432047 / Symmetry type: POINT |