6X5G

Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and LRRC7 inhibitory domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

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Ligand Structure Quality Assessment 


This is version 2.1 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: 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 ...

    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. Electronic address: mstratton@umass.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Calcium/calmodulin-dependent protein kinase type II subunit alphaA268Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UQM7
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Leucine-rich repeat-containing protein 7B22Homo sapiensMutation(s): 0 
Gene Names: LRRC7KIAA1365LAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96NW7 (Homo sapiens)
Explore Q96NW7 
Go to UniProtKB:  Q96NW7
PHAROS:  Q96NW7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96NW7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCN
Query on BCN

Download Ideal Coordinates CCD File 
E [auth A]BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.29α = 90
b = 66.173β = 99.78
c = 61.706γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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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, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2022-08-10
    Changes: Database references