7YA5 | pdb_00007ya5

Crystal structure analysis of cp1 bound BCL2/G101V

• PDB DOI: https://doi.org/10.2210/pdb7YA5/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-06-27 Released: 2023-11-15 
• Deposition Author(s): Li, F.W., Liu, C., Wu, C.L., Wu, D.L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.243 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Cyclic peptides discriminate BCL-2 and its clinical mutants from BCL-X L by engaging a single-residue discrepancy.

Li, F., Liu, J., Liu, C., Liu, Z., Peng, X., Huang, Y., Chen, X., Sun, X., Wang, S., Chen, W., Xiong, D., Diao, X., Wang, S., Zhuang, J., Wu, C., Wu, D.

(2024) Nat Commun 15: 1476-1476

• PubMed: 38368459 
• DOI: https://doi.org/10.1038/s41467-024-45848-1
• Primary Citation Related Structures: 
  7Y8D, 7Y90, 7Y99, 7YA5, 7YAA, 7YB7


• PubMed Abstract: 
  

  Overexpressed pro-survival B-cell lymphoma-2 (BCL-2) family proteins BCL-2 and BCL-X _L can render tumor cells malignant. Leukemia drug venetoclax is currently the only approved selective BCL-2 inhibitor. However, its application has led to an emergence of resistant mutations, calling for drugs with an innovative mechanism of action. Herein we present cyclic peptides (CPs) with nanomolar-level binding affinities to BCL-2 or BCL-X _L , and further reveal the structural and functional mechanisms of how these CPs target two proteins in a fashion that is remarkably different from traditional small-molecule inhibitors. In addition, these CPs can bind to the venetoclax-resistant clinical BCL-2 mutants with similar affinities as to the wild-type protein. Furthermore, we identify a single-residue discrepancy between BCL-2 D111 and BCL-X _L A104 as a molecular "switch" that can differently engage CPs. Our study suggests that CPs may inhibit BCL-2 or BCL-X _L by delicately modulating protein-protein interactions, potentially benefiting the development of next-generation therapeutics.

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Organizational Affiliation: 
• Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China. [e-mail].
The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
Shanghai Zelixir Biotech Company Ltd., Shanghai, 200030, China.
Shanghai Immune Therapy Institute, Shanghai Jiao Tong University School of Medicine-Affiliated Renji Hospital, Shanghai, 200127, China.
Xiamen Lifeint Technology Company Ltd., Xiamen, 361005, China.
Marine College, Shandong University, Weihai, 264209, China.
The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China. [e-mail].
Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.25 kDa 
• Atom Count: 1,384 
• Modeled Residue Count: 151 
• Deposited Residue Count: 178 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apoptosis regulator Bcl-2	A	166	Homo sapiens	Mutation(s): 1  Gene Names: BCL2
UniProt & NIH Common Fund Data Resources
Find proteins for P10415 (Homo sapiens) Explore P10415  Go to UniProtKB:  P10415
PHAROS:  P10415 GTEx:  ENSG00000171791

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cp1 peptide	B	12	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JFF (Subject of Investigation/LOI)	C [auth B]	(2R)-3-[2-(aminomethyl)-3-azanyl-1-[4-[2-(2-chloranylethanoylamino)ethylcarbamoyl]phenyl]prop-1-enyl]sulfanyl-2-(carboxyamino)propanoic acid C19 H26 Cl N5 O6 S SHRIZMDECXYRNC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.243 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.726	α = 90
b = 50.054	β = 107.58
c = 48.693	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-15 
Deposition Author(s): Li, F.W., Liu, C., Wu, C.L., Wu, D.L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2023-11-15
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Database references
• Version 1.2: 2024-10-23
  Changes: Structure summary