7SHQ | pdb_00007shq

Structure of a functional construct of eukaryotic elongation factor 2 kinase in complex with calmodulin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 
    0.252 (Depositor), 0.265 (DCC) 
  • R-Value Work: 
    0.229 (Depositor) 
  • R-Value Observed: 
    0.230 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7SHQ

This is version 1.3 of the entry. See complete history

Literature

Structural basis for the calmodulin-mediated activation of eukaryotic elongation factor 2 kinase.

Piserchio, A.Isiorho, E.A.Long, K.Bohanon, A.L.Kumar, E.A.Will, N.Jeruzalmi, D.Dalby, K.N.Ghose, R.

(2022) Sci Adv 8: eabo2039-eabo2039

  • DOI: https://doi.org/10.1126/sciadv.abo2039
  • Primary Citation Related Structures: 
    7SHQ

  • PubMed Abstract: 

    Translation is a tightly regulated process that ensures optimal protein quality and enables adaptation to energy/nutrient availability. The α-kinase eukaryotic elongation factor 2 kinase (eEF-2K), a key regulator of translation, specifically phosphorylates the guanosine triphosphatase eEF-2, thereby reducing its affinity for the ribosome and suppressing the elongation phase of protein synthesis. eEF-2K activation requires calmodulin binding and autophosphorylation at the primary stimulatory site, T348. Biochemical studies predict a calmodulin-mediated activation mechanism for eEF-2K distinct from other calmodulin-dependent kinases. Here, we resolve the atomic details of this mechanism through a 2.3-Å crystal structure of the heterodimeric complex of calmodulin and the functional core of eEF-2K (eEF-2K TR ). This structure, which represents the activated T348-phosphorylated state of eEF-2K TR , highlights an intimate association of the kinase with the calmodulin C-lobe, creating an "activation spine" that connects its amino-terminal calmodulin-targeting motif to its active site through a conserved regulatory element.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA.

Macromolecule Content 

  • Total Structure Weight: 77.37 kDa 
  • Atom Count: 5,268 
  • Modeled Residue Count: 637 
  • Deposited Residue Count: 679 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic elongation factor 2 kinase,Eukaryotic elongation factor 2 kinase531Homo sapiensMutation(s): 0 
Gene Names: EEF2K
EC: 2.7.11.20
UniProt & NIH Common Fund Data Resources
Find proteins for O00418 (Homo sapiens)
Explore O00418 
Go to UniProtKB:  O00418
PHAROS:  O00418
GTEx:  ENSG00000103319 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00418
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Calmodulin-1148Homo sapiensMutation(s): 0 
Gene Names: CALM1CALMCAMCAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens)
Explore P0DP23 
Go to UniProtKB:  P0DP23
PHAROS:  P0DP23
GTEx:  ENSG00000198668 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP23
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
(Subject of Investigation/LOI)

Query on CA



Download:Ideal Coordinates CCD File
F [auth B],
G [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
H [auth B],
I [auth B],
J [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free:  0.252 (Depositor), 0.265 (DCC) 
  • R-Value Work:  0.229 (Depositor) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.495α = 90
b = 58.495β = 90
c = 365.779γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
ISOLDErefinement
Cootmodel building
MR-Rosettaphasing
autoPROCdata scaling
autoPROCdata reduction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM084278

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release
  • Version 1.1: 2022-08-03
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary