7C2P | pdb_00007c2p

Structure of Egk Peptide

• PDB DOI: https://doi.org/10.2210/pdb7C2P/pdb

• Classification: PROTEIN BINDING
• Organism(s): Elaeis guineensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-05-08 Released: 2020-09-09 
• Deposition Author(s): El Sahili, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.263 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.243 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Modulation of Lymphocyte Potassium Channel KV1.3 by Membrane-Penetrating, Joint-Targeting Immunomodulatory Plant Defensin.

Ong, S.T., Bajaj, S., Tanner, M.R., Chang, S.C., Krishnarjuna, B., Ng, X.R., Morales, R.A.V., Chen, M.W., Luo, D., Patel, D., Yasmin, S., Ng, J.J.H., Zhuang, Z., Nguyen, H.M., El Sahili, A., Lescar, J., Patil, R., Charman, S.A., Robins, E.G., Goggi, J.L., Tan, P.W., Sadasivam, P., Ramasamy, B., Hartimath, S.V., Dhawan, V., Bednenko, J., Colussi, P., Wulff, H., Pennington, M.W., Kuyucak, S., Norton, R.S., Beeton, C., Chandy, K.G.

(2020) Acs Pharmacol Transl Sci 3: 720-736

• PubMed: 32832873 
• DOI: https://doi.org/10.1021/acsptsci.0c00035
• Primary Citation Related Structures: 
  7C2P, 7C31


• PubMed Abstract: 
  

  We describe a cysteine-rich, membrane-penetrating, joint-targeting, and remarkably stable peptide, EgK5, that modulates voltage-gated K _V 1.3 potassium channels in T lymphocytes by a distinctive mechanism. EgK5 enters plasma membranes and binds to K _V 1.3, causing current run-down by a phosphatidylinositol 4,5-bisphosphate-dependent mechanism. EgK5 exhibits selectivity for K _V 1.3 over other channels, receptors, transporters, and enzymes. EgK5 suppresses antigen-triggered proliferation of effector memory T cells, a subset enriched among pathogenic autoreactive T cells in autoimmune disease. PET-CT imaging with ¹⁸ F-labeled EgK5 shows accumulation of the peptide in large and small joints of rodents. In keeping with its arthrotropism, EgK5 treats disease in a rat model of rheumatoid arthritis. It was also effective in treating disease in a rat model of atopic dermatitis. No signs of toxicity are observed at 10-100 times the in vivo dose. EgK5 shows promise for clinical development as a therapeutic for autoimmune diseases.

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Organizational Affiliation: 
• Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Experimental Medicine Building, 59 Nanyang Drive, Singapore 636921.
Department of Molecular Physiology and Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, United States.
Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia.
School of Physics, University of Sydney, Sydney, New South Wales 2006, Australia.
Department of Pharmacology, University of California, Davis, California 95616, United States.
School of Biological Sciences, Nanyang Institute of Structural Biology, Experimental Medicine building, Singapore 636921.
Centre for Drug Candidate Optimisation, Monash University, Parkville, Victoria 3052, Australia.
Singapore Bioimaging Consortium, Agency for Science, Technology and Research (A Star), Singapore 138667.
Singapore Bioimaging Consortium, NUS Clinical Imaging Research Centre (CIRC), Centre for Life Sciences, Singapore 117599.
Peptides International, Inc., Louisville, Kentucky 40269, United States.
AmbioPharm Inc., North Augusta, South Carolina 29842, United States.
TetraGenetics Inc, Arlington, Massachusetts 02474, United States.
ARC Centre for Fragment-Based Design, Monash University, Parkville, Victoria 3052, Australia.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.41 kDa 
• Atom Count: 1,507 
• Modeled Residue Count: 188 
• Deposited Residue Count: 188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plant defensing Egk	A, B, C, D	47	Elaeis guineensis	Mutation(s): 0
UniProt
Find proteins for A0A7M4DUG7 (Elaeis guineensis var. tenera) Explore A0A7M4DUG7  Go to UniProtKB:  A0A7M4DUG7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.263 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.243 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.84	α = 83.76
b = 37.92	β = 78.35
c = 54.77	γ = 70.22

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-09-09 
Deposition Author(s): El Sahili, A.

Revision History  

• Version 1.0: 2020-09-09
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary