4EAG | pdb_00004eag

Co-crystal structure of an chimeric AMPK core with ATP

PDB DOI: https://doi.org/10.2210/pdb4EAG/pdb

Classification: TRANSFERASE
Organism(s): Drosophila melanogaster, 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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.252 (Depositor), 0.250 (DCC)
R-Value Work:
0.208 (Depositor), 0.210 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 63.3 kDa
Atom Count: 3,755
Modelled Residue Count: 445
Deposited Residue Count: 545
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EG:132E8.2 protein	A	130	Drosophila melanogaster	Mutation(s): 0 Gene Names: SNF1A, EG:132E8.2, SNF1A-RA, CG3051, Dmel_CG3051 EC: 2.7.11 (PDB Primary Data), 2.7.11.16 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt
Find proteins for O18645 (Drosophila melanogaster) Explore O18645 Go to UniProtKB: O18645
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O18645
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-activated protein kinase subunit beta-1	B	85	Rattus norvegicus	Mutation(s): 0 Gene Names: Prkab1
UniProt
Find proteins for P80386 (Rattus norvegicus) Explore P80386 Go to UniProtKB: P80386
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80386
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80385
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain D [auth C] SDF format, chain E [auth C] MOL2 format, chain D [auth C] MOL2 format, chain E [auth C] mmCIF format, chain D [auth C] mmCIF format, chain E [auth C]	D [auth C], E [auth C]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain D [auth C] Focus chain E [auth C] Interactions & Density Focus chain D [auth C] Focus chain E [auth C]
TAM Query on TAM Download Ideal Coordinates CCD File SDF format, chain F [auth C] MOL2 format, chain F [auth C] mmCIF format, chain F [auth C]	F [auth C]	TRIS(HYDROXYETHYL)AMINOMETHANE C₇ H₁₇ N O₃ GKODZWOPPOTFGA-UHFFFAOYSA-N		Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.252 (Depositor), 0.250 (DCC)
R-Value Work: 0.208 (Depositor), 0.210 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.668	α = 90
b = 151.283	β = 90
c = 109.323	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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-06-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-06-06
Type: Initial release
Version 1.1: 2014-03-12
Changes: Database references
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description