4EAL

Co-crystal of AMPK core with ATP soaked with AMP

• PDB DOI: https://doi.org/10.2210/pdb4EAL/pdb

• Classification: TRANSFERASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-22 Released: 2012-06-06 
• Deposition Author(s): Chen, L., Wang, J., Zhang, Y.-Y., Yan, S.F., Neumann, D., Schlattner, U., Wang, Z.-X., Wu, J.-W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.277 
• R-Value Work: 0.232 
• R-Value Observed: 0.235 

Starting Model: experimental

Literature

AMP-activated protein kinase undergoes nucleotide-dependent conformational changes

Chen, L., Wang, J., Zhang, Y.-Y., Yan, S.F., Neumann, D., Schlattner, U., Wang, Z.-X., Wu, J.-W.

(2012) Nat Struct Mol Biol 19: 716-718

• PubMed: 22659875 
• DOI: https://doi.org/10.1038/nsmb.2319
• Primary Citation of Related Structures:  
  4EAG, 4EAI, 4EAJ, 4EAK, 4EAL


• PubMed Abstract: 
  

  The energy sensor AMP-activated protein kinase (AMPK) is a heterotrimeric complex that is allosterically activated by AMP binding to the γ subunit. Cocrystal structures of the mammalian AMPK core reveal occlusion of nucleotide-binding site 3 of the γ subunit in the presence of ATP. However, site 3 is occupied in the presence of AMP. Mutagenesis studies indicate that sites 3 and 4 are important for AMPK allosteric activation.

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Organizational Affiliation: 

MOE Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 58.36 kDa 
• Atom Count: 3,493 
• Modelled Residue Count: 419 
• Deposited Residue Count: 508 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-activated protein kinase catalytic subunit alpha-1	A	106	Rattus norvegicus	Mutation(s): 0  Gene Names: Prkaa1, Ampk1 EC: 2.7.11.1 (PDB Primary Data), 2.7.11.27 (PDB Primary Data), 2.7.11.31 (PDB Primary Data), 2.7.11.26 (PDB Primary Data)
UniProt
Find proteins for P54645 (Rattus norvegicus) Explore P54645  Go to UniProtKB:  P54645

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-activated protein kinase subunit beta-1	B	72	Rattus norvegicus	Mutation(s): 0  Gene Names: Prkab1
UniProt
Find proteins for P80386 (Rattus norvegicus) Explore P80386  Go to UniProtKB:  P80386

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-activated protein kinase subunit gamma-1	C	330	Rattus norvegicus	Mutation(s): 0  Gene Names: Prkag1
UniProt
Find proteins for P80385 (Rattus norvegicus) Explore P80385  Go to UniProtKB:  P80385

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	D [auth C], E [auth C]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.277 
• R-Value Work: 0.232 
• R-Value Observed: 0.235 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 175.85	α = 90
b = 40.503	β = 105.53
c = 77.738	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-06 
Deposition Author(s): Chen, L., Wang, J., Zhang, Y.-Y., Yan, S.F., Neumann, D., Schlattner, U., Wang, Z.-X., Wu, J.-W.

Revision History  

• Version 1.0: 2012-06-06
  Type: Initial release
  
• Version 1.1: 2014-03-12
  Changes: Database references
• Version 1.2: 2017-06-21
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description