7L92

C1B domain of Protein kinase C in complex with diacylglycerol and dodecyl 2-(trimethylammonio)ethyl phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural anatomy of Protein Kinase C C1 domain interactions with diacylglycerol and other agonists.

Katti, S.S.Krieger, I.V.Ann, J.Lee, J.Sacchettini, J.C.Igumenova, T.I.

(2022) Nat Commun 13: 2695-2695

  • DOI: https://doi.org/10.1038/s41467-022-30389-2
  • Primary Citation of Related Structures:  
    7KND, 7KNJ, 7KO6, 7L92, 7LCB, 7LEO, 7LF3

  • PubMed Abstract: 

    Diacylglycerol (DAG) is a versatile lipid whose 1,2-sn-stereoisomer serves both as second messenger in signal transduction pathways that control vital cellular processes, and as metabolic precursor for downstream signaling lipids such as phosphatidic acid. Effector proteins translocate to available DAG pools in the membranes by using conserved homology 1 (C1) domains as DAG-sensing modules. Yet, how C1 domains recognize and capture DAG in the complex environment of a biological membrane has remained unresolved for the 40 years since the discovery of Protein Kinase C (PKC) as the first member of the DAG effector cohort. Herein, we report the high-resolution crystal structures of a C1 domain (C1B from PKCδ) complexed to DAG and to each of four potent PKC agonists that produce different biological readouts and that command intense therapeutic interest. This structural information details the mechanisms of stereospecific recognition of DAG by the C1 domains, the functional properties of the lipid-binding site, and the identities of the key residues required for the recognition and capture of DAG and exogenous agonists. Moreover, the structures of the five C1 domain complexes provide the high-resolution guides for the design of agents that modulate the activities of DAG effector proteins.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77840, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein kinase C delta type53Rattus norvegicusMutation(s): 0 
Gene Names: PrkcdrCG_42255
EC: 2.7.11.13
Membrane Entity: Yes 
UniProt
Find proteins for P09215 (Rattus norvegicus)
Explore P09215 
Go to UniProtKB:  P09215
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09215
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGA
Query on DGA

Download Ideal Coordinates CCD File 
BA [auth M]
FA [auth P]
JA [auth S]
K [auth A]
L [auth A]
BA [auth M],
FA [auth P],
JA [auth S],
K [auth A],
L [auth A],
OA [auth V],
P [auth D],
T [auth G],
U [auth G],
X [auth J]
DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
DPV
Query on DPV

Download Ideal Coordinates CCD File 
CA [auth M]
GA [auth P]
KA [auth S]
PA [auth V]
Q [auth D]
CA [auth M],
GA [auth P],
KA [auth S],
PA [auth V],
Q [auth D],
Y [auth J]
dodecyl 2-(trimethylammonio)ethyl phosphate
C17 H38 N O4 P
QBHFVMDLPTZDOI-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth M]
DA [auth P]
EA [auth P]
HA [auth S]
I [auth A]
AA [auth M],
DA [auth P],
EA [auth P],
HA [auth S],
I [auth A],
IA [auth S],
J [auth A],
MA [auth V],
N [auth D],
NA [auth V],
O [auth D],
R [auth G],
S [auth G],
V [auth J],
W [auth J],
Z [auth M]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EOH
Query on EOH

Download Ideal Coordinates CCD File 
LA [auth S],
M [auth A]
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.068α = 90
b = 89.068β = 90
c = 218.679γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM108998

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-04
    Type: Initial release
  • Version 1.1: 2022-07-13
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description