+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36216 | |||||||||
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Title | local map of hPhK alpha-gamma subcomplex in active state | |||||||||
Map data | ||||||||||
Sample |
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Keywords | local map of hPhK alpha-gamma subcomplex / CYTOSOLIC PROTEIN | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Yang XK / Xiao JY | |||||||||
Funding support | China, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36216.map.gz | 328.1 MB | EMDB map data format | |
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Header (meta data) | emd-36216-v30.xml emd-36216.xml | 11.1 KB 11.1 KB | Display Display | EMDB header |
Images | emd_36216.png | 9.9 KB | ||
Filedesc metadata | emd-36216.cif.gz | 3.5 KB | ||
Others | emd_36216_half_map_1.map.gz emd_36216_half_map_2.map.gz | 322 MB 322 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36216 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36216 | HTTPS FTP |
-Related structure data
Related structure data | 8xy7MC 8jfkC 8jflC 8xyaC 8xybC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_36216.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_36216_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36216_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : local map of hPhK alpha-gamma subcomplex
Entire | Name: local map of hPhK alpha-gamma subcomplex |
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Components |
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-Supramolecule #1: local map of hPhK alpha-gamma subcomplex
Supramolecule | Name: local map of hPhK alpha-gamma subcomplex / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8.2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: OTHER / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.1 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.5 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 432047 |