8JFK

PhK holoenzyme in inactive state, muscle isoform


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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

Architecture and activation of human muscle phosphorylase kinase.

Yang, X.Zhu, M.Lu, X.Wang, Y.Xiao, J.

(2024) Nat Commun 15: 2719-2719

  • DOI: https://doi.org/10.1038/s41467-024-47049-2
  • Primary Citation of Related Structures:  
    8JFK, 8JFL, 8XY7, 8XYA, 8XYB

  • PubMed 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 poorly understood. Here we present the high-resolution cryo-electron microscopy structures of human muscle PhK. The 1.3-megadalton PhK α 4 β 4 γ 4 δ 4 hexadecamer consists of a tetramer of tetramer, wherein four αβγδ modules are connected by the central β 4 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 2+ -free calmodulin (δ-subunit) binds to the γ-subunit in a compact conformation. Upon binding of Ca 2+ , 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.


  • Organizational Affiliation

    State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, P.R. China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphorylase b kinase regulatory subunit betaA [auth B],
D [auth N],
E [auth J],
G [auth F]
1,093Homo sapiensMutation(s): 0 
Gene Names: PHKB
UniProt & NIH Common Fund Data Resources
Find proteins for Q93100 (Homo sapiens)
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PHAROS:  Q93100
GTEx:  ENSG00000102893 
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UniProt GroupQ93100
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoformB [auth M],
C [auth A],
F [auth I],
H [auth E]
1,223Homo sapiensMutation(s): 0 
Gene Names: PHKA1PHKA
UniProt & NIH Common Fund Data Resources
Find proteins for P46020 (Homo sapiens)
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PHAROS:  P46020
GTEx:  ENSG00000067177 
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UniProt GroupP46020
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Calmodulin-1I [auth D],
K [auth H],
M [auth L],
O [auth P]
149Homo sapiensMutation(s): 0 
Gene Names: CALM1CALMCAMCAM1
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Find proteins for P0DP23 (Homo sapiens)
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PHAROS:  P0DP23
GTEx:  ENSG00000198668 
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UniProt GroupP0DP23
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoformJ [auth C],
L [auth G],
N [auth K],
P [auth O]
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)
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Find proteins for Q16816 (Homo sapiens)
Explore Q16816 
Go to UniProtKB:  Q16816
PHAROS:  Q16816
GTEx:  ENSG00000164776 
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UniProt GroupQ16816
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-03
    Type: Initial release
  • Version 1.1: 2024-04-10
    Changes: Database references