7C8E | pdb_00007c8e

Crystal Structure of 14-3-3 epsilon with 9J10 peptide

• PDB DOI: https://doi.org/10.2210/pdb7C8E/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens, Streptomyces avermitilis MA-4680 = NBRC 14893
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-05-30 Released: 2021-06-02 
• Deposition Author(s): Mathivanan, S., Sudhakar, S., Bairy, S., Kamariah, N., Venkitaraman, A.
• Funding Organization(s): Department of Biotechnology (DBT, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.16 Å
• R-Value Free: 
  0.271 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Target identification for small-molecule discovery in the FOXO3a tumor-suppressor pathway using a biodiverse peptide library.

Emery, A., Hardwick, B.S., Crooks, A.T., Milech, N., Watt, P.M., Mithra, C., Kumar, V., Giridharan, S., Sadasivam, G., Mathivanan, S., Sudhakar, S., Bairy, S., Bharatham, K., Hurakadli, M.A., Prasad, T.K., Kamariah, N., Muellner, M., Coelho, M., Torrance, C.J., McKenzie, G.J., Venkitaraman, A.R.

(2021) Cell Chem Biol 28: 1602-1615.e9

• PubMed: 34111400 
• DOI: https://doi.org/10.1016/j.chembiol.2021.05.009
• Primary Citation Related Structures: 
  7C8E


• PubMed Abstract: 
  

  Genetic screening technologies to identify and validate macromolecular interactions (MMIs) essential for complex pathways remain an important unmet need for systems biology and therapeutics development. Here, we use a library of peptides from diverse prokaryal genomes to screen MMIs promoting the nuclear relocalization of Forkhead Box O3 (FOXO3a), a tumor suppressor more frequently inactivated by post-translational modification than mutation. A hit peptide engages the 14-3-3 family of signal regulators through a phosphorylation-dependent interaction, modulates FOXO3a-mediated transcription, and suppresses cancer cell growth. In a crystal structure, the hit peptide occupies the phosphopeptide-binding groove of 14-3-3ε in a conformation distinct from its natural peptide substrates. A biophysical screen identifies drug-like small molecules that displace the hit peptide from 14-3-3ε, providing starting points for structure-guided development. Our findings exemplify "protein interference," an approach using evolutionarily diverse, natural peptides to rapidly identify, validate, and develop chemical probes against MMIs essential for complex cellular phenotypes.

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Organizational Affiliation: 
• Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK.
Telethon Kids Institute, Centre for Child Health Research, University of Western Australia & PYC Therapeutics Limited, Nedlands, WA 6009, Australia.
Center for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore 560065, India.
PhoreMost Ltd., Babraham Research Campus, Cambridge CB22 3AT, UK.
Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK; PhoreMost Ltd., Babraham Research Campus, Cambridge CB22 3AT, UK.
Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK; Center for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore 560065, India; PhoreMost Ltd., Babraham Research Campus, Cambridge CB22 3AT, UK. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 63.51 kDa 
• Atom Count: 3,735 
• Modeled Residue Count: 473 
• Deposited Residue Count: 556 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein epsilon	A, B	266	Homo sapiens	Mutation(s): 0  Gene Names: YWHAE
UniProt & NIH Common Fund Data Resources
Find proteins for P62258 (Homo sapiens) Explore P62258  Go to UniProtKB:  P62258
PHAROS:  P62258 GTEx:  ENSG00000108953

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
9J10	C, D	12	Streptomyces avermitilis MA-4680 = NBRC 14893	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS (Subject of Investigation/LOI)	E [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	C, D	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.16 Å
• R-Value Free:  0.271 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.47	α = 90
b = 83.35	β = 90
c = 118.81	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-06-02 
Deposition Author(s): Mathivanan, S., Sudhakar, S., Bairy, S., Kamariah, N., Venkitaraman, A.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	--

Revision History  

• Version 1.0: 2021-06-02
  Type: Initial release
  
• Version 1.1: 2021-06-30
  Changes: Database references
• Version 1.2: 2021-12-08
  Changes: Database references
• Version 1.3: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.4: 2024-10-09
  Changes: Structure summary