Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: fluorescence resonance energy transfer

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17.22 kDa 
• Atom Count: 1194 
• Modelled Residue Count: 144 
• Deposited Residue Count: 148 
• Unique protein chains: 1

6OS4

Calmodulin in complex with farnesyl cysteine methyl ester

• PDB DOI: 10.2210/pdb6OS4/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-05-01 Released: 2020-04-08 
• Deposition Author(s): Grant, B.M.M., Enomoto, M., Lee, K.Y., Back, S.I., Gebregiworgis, T., Ishiyama, N., Ikura, M., Marshall, C.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.225 
• R-Value Work: 0.191 
• R-Value Observed: 0.195 

Literature

Calmodulin disrupts plasma membrane localization of farnesylated KRAS4b by sequestering its lipid moiety.

Grant, B.M.M., Enomoto, M., Back, S.I., Lee, K.Y., Gebregiworgis, T., Ishiyama, N., Ikura, M., Marshall, C.B.

(2020) Sci Signal 13

• PubMed: 32234958 
• DOI: 10.1126/scisignal.aaz0344
• Primary Citation of Related Structures:  
  6OS4


• PubMed Abstract: 
  

KRAS4b is a small guanosine triphosphatase (GTPase) protein that regulates several signal transduction pathways that underlie cell proliferation, differentiation, and survival. KRAS4b function requires prenylation of its C terminus and recruitment to the plasma membrane, where KRAS4b activates effector proteins including the RAF family of kinases. The Ca ²⁺ -sensing protein calmodulin (CaM) has been suggested to regulate the localization of KRAS4b through direct, Ca ²⁺ -dependent interaction, but how CaM and KRAS4b functionally interact is controversial. Here, we determined a crystal structure, which was supported by solution nuclear magnetic resonance (NMR), that revealed the sequestration of the prenyl moiety of KRAS4b in the hydrophobic pocket of the C-terminal lobe of Ca ²⁺ -bound CaM. Our engineered fluorescence resonance energy transfer (FRET)-based biosensor probes (CaMeRAS) showed that, upon stimulation of Ca ²⁺ influx by extracellular ligands, KRAS4b reversibly translocated in a Ca ²⁺ -CaM-dependent manner from the plasma membrane to the cytoplasm in live HeLa and HEK293 cells. These results reveal a mechanism underlying the inhibition of KRAS4b activity by Ca ²⁺ signaling pathways.

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Organizational Affiliation: 

Princess Margaret Cancer Center, University Health Network, Toronto, Ontario M5G 1L7, Canada. [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin-1	A	148	Homo sapiens	Mutation(s): 0  Gene Names: CALM1, CALM, CAM, CAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens) Explore P0DP23  Go to UniProtKB:  P0DP23
PHAROS:  P0DP23 GTEx:  ENSG00000198668

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5U0 (Subject of Investigation/LOI)	F [auth A]	s-farnesyl-l-cysteine methyl ester C19 H33 N O2 S SIEHZFPZQUNSAS-GCVUPTOQSA-N
CA	B [auth A], C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.225 
• R-Value Work: 0.191 
• R-Value Observed: 0.195 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.379	α = 90
b = 40.379	β = 90
c = 338.137	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-05-01 
• Released Date: 2020-04-08 
Deposition Author(s): Grant, B.M.M., Enomoto, M., Lee, K.Y., Back, S.I., Gebregiworgis, T., Ishiyama, N., Ikura, M., Marshall, C.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	FDN-154284

Revision History  

• Version 1.0: 2020-04-08
  Type: Initial release
  
• Version 1.1: 2020-04-15
  Changes: Database references