8Z5R | pdb_00008z5r

human phosphorylase kinase alpha/gamma/delta subcomplex - phosphorylation and Ca2+ bound state

  • Classification: CYTOSOLIC PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2024-04-18 Released: 2025-04-23 
  • Deposition Author(s): Ma, R., Yan, K.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular basis for the regulation of human phosphorylase kinase by phosphorylation and Ca 2.

Ma, R.Du, B.Shi, C.Wang, L.Zeng, F.Han, J.Guan, H.Wang, Y.Yan, K.

(2025) Nat Commun 16: 3020-3020

  • DOI: https://doi.org/10.1038/s41467-025-58363-8
  • Primary Citation of Related Structures:  
    8Z5M, 8Z5P, 8Z5Q, 8Z5R, 8Z5T

  • PubMed Abstract: 

    Phosphorylase kinase (PhK) regulates the degradation of glycogen by integrating diverse signals, providing energy to the organism. Dysfunctional mutations may directly lead to Glycogen Storage Disease type IX (GSD IX), whereas the abnormal expression of PhK is also associated with tumors. Here, we use cryo-electron microscopy (cryo-EM) to resolve its near-atomic structures in the inactive and active states. These structures reveal the interactions and relative locations of the four subunits (αβγδ) within the PhK complex. Phosphorylated α and β subunits induce PhK to present a more compact state, while Ca 2+ causes sliding of the δ subunit along the helix of the γ subunit. Both actions synergistically activate PhK by enabling the de-inhibition of the γ subunit. We also identified different binding modes between PhK and its substrate, glycogen phosphorylase (GP), in two distinct states, using cross-linking mass spectrometry (XL-MS). This study provides valuable insights into the regulatory mechanisms of PhK, thereby enhancing our understanding of GSD IX and its implications in tumorigenesis.


  • Organizational Affiliation
    • Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform1,223Homo sapiensMutation(s): 0 
Gene Names: PHKA1PHKA
UniProt & NIH Common Fund Data Resources
Find proteins for P46020 (Homo sapiens)
Explore P46020 
Go to UniProtKB:  P46020
PHAROS:  P46020
GTEx:  ENSG00000067177 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46020
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoformB [auth C]387Homo sapiensMutation(s): 0 
Gene Names: PHKG1PHKG
EC: 2.7.11.19 (PDB Primary Data), 2.7.11.1 (PDB Primary Data), 2.7.11.26 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q16816 (Homo sapiens)
Explore Q16816 
Go to UniProtKB:  Q16816
PHAROS:  Q16816
GTEx:  ENSG00000164776 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16816
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Calmodulin-3C [auth D]168Homo sapiensMutation(s): 0 
Gene Names: CALM3CALML2CAM3CAMCCAMIII
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP25 (Homo sapiens)
Explore P0DP25 
Go to UniProtKB:  P0DP25
PHAROS:  P0DP25
GTEx:  ENSG00000160014 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP25
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
D [auth C]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2025-04-23 
  • Deposition Author(s): Ma, R., Yan, K.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32271251

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release
  • Version 1.1: 2025-09-24
    Changes: Data collection, Database references