7KL1

Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B(S1303D)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

CaMKII binds both substrates and activators at the active site.

Ozden, C.Sloutsky, R.Mitsugi, T.Santos, N.Agnello, E.Gaubitz, C.Foster, J.Lapinskas, E.Esposito, E.A.Saneyoshi, T.Kelch, B.A.Garman, S.C.Hayashi, Y.Stratton, M.M.

(2022) Cell Rep 40: 111064-111064

  • DOI: https://doi.org/10.1016/j.celrep.2022.111064
  • Primary Citation of Related Structures:  
    6X5G, 6X5Q, 7KL0, 7KL1, 7UIQ, 7UIR, 7UIS, 7UJP, 7UJQ, 7UJR, 7UJS, 7UJT

  • PubMed Abstract: 

    Ca 2+ /calmodulin-dependent protein kinase II (CaMKII) is a signaling protein required for long-term memory. When activated by Ca 2+ /CaM, it sustains activity even after the Ca 2+ dissipates. In addition to the well-known autophosphorylation-mediated mechanism, interaction with specific binding partners also persistently activates CaMKII. A long-standing model invokes two distinct S and T sites. If an interactor binds at the T-site, then it will preclude autoinhibition and allow substrates to be phosphorylated at the S site. Here, we specifically test this model with X-ray crystallography, molecular dynamics simulations, and biochemistry. Our data are inconsistent with this model. Co-crystal structures of four different activators or substrates show that they all bind to a single continuous site across the kinase domain. We propose a mechanistic model where persistent CaMKII activity is facilitated by high-affinity binding partners that kinetically compete with autoinhibition by the regulatory segment to allow substrate phosphorylation.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA; Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calcium/calmodulin-dependent protein kinase type II subunit alpha
A, B
268Homo sapiensMutation(s): 2 
Gene Names: CAMK2ACAMKAKIAA0968
EC: 2.7.11.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQM7 (Homo sapiens)
Explore Q9UQM7 
Go to UniProtKB:  Q9UQM7
PHAROS:  Q9UQM7
GTEx:  ENSG00000070808 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UQM7
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 2B
C, D
22Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13224 (Homo sapiens)
Explore Q13224 
Go to UniProtKB:  Q13224
PHAROS:  Q13224
GTEx:  ENSG00000273079 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13224
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
J [auth C],
K [auth D]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
H [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.893α = 90
b = 92.133β = 90
c = 91.338γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 2.0: 2022-04-06
    Type: Coordinate replacement
    Reason: Atoms with unrealistic or zero occupancies
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Experimental preparation, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2022-08-10
    Changes: Database references
  • Version 2.2: 2023-10-18
    Changes: Data collection, Refinement description