6QCI | pdb_00006qci

Structure of XIAP-BIR1 V86E mutant

• PDB DOI: https://doi.org/10.2210/pdb6QCI/pdb

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


• Deposited: 2018-12-28 Released: 2019-05-01 
• Deposition Author(s): Sorrentino, L., Cossu, F., Milani, M., Mastrangelo, E.
• Funding Organization(s): Italian Association for Cancer Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.303 (Depositor), 0.301 (DCC) 
• R-Value Work: 
  0.264 (Depositor), 0.266 (DCC) 
• R-Value Observed: 
  0.266 (Depositor) 

Starting Model: experimental

Literature

Structure-Activity Relationship of NF023 Derivatives Binding to XIAP-BIR1.

Sorrentino, L., Cossu, F., Milani, M., Malkoc, B., Huang, W.C., Tsay, S.C., Ru Hwu, J., Mastrangelo, E.

(2019) ChemistryOpen 8: 476-482

• PubMed: 31011505 
• DOI: https://doi.org/10.1002/open.201900059
• Primary Citation Related Structures: 
  6GJW, 6QCI


• PubMed Abstract: 
  

  Inhibitors of Apoptosis Proteins (IAPs) are conserved E3-ligases that ubiquitylate substrates to prevent apoptosis and activate the NF-kB survival pathway, often deregulated in cancer. IAPs-mediated regulation of NF-kB signaling is based on the formation of protein complexes by their type-I BIR domains. The XIAP-BIR1 domain dimerizes to bind two TAB1 monomers, leading to downstream NF-kB activation. Thus, impairment of XIAP-BIR1 dimerization could represent a novel strategy to hamper cell survival in cancer. To this aim, we previously reported NF023 as a potential inhibitor of XIAP-BIR1 dimerization. Here we present a thorough analysis of NF023 binding to XIAP-BIR1 through biochemical, biophysical and structural data. The results obtained indicate that XIAP-BIR1 dimerization interface is involved in NF023 binding, and that NF023 overall symmetry and the chemical features of its central moiety are essential for an efficient interaction with the protein. Such strategy provides original hints for the development of novel BIR1-specific compounds as pro-apoptotic agents.

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Organizational Affiliation: 
• CNR-IBF Via Celoria 26 I-20133 Milano Italy.
Department of Biosciences Università di Milano Via Celoria 26 I-20133 Milano Italy.
Department of Chemistry & Frontier Research Center on Fundamental and Applied Sciences of Matters National Tsing Hua University Hsinchu 30013 Taiwan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

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: 49.96 kDa 
• Atom Count: 2,453 
• Modeled Residue Count: 300 
• Deposited Residue Count: 444 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase XIAP	A, B, C, D	111	Homo sapiens	Mutation(s): 1  Gene Names: XIAP, API3, BIRC4, IAP3 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for P98170 (Homo sapiens) Explore P98170  Go to UniProtKB:  P98170
PHAROS:  P98170 GTEx:  ENSG00000101966

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	I [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	E [auth A], G [auth B], H [auth C], J [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	F [auth A], K [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.303 (Depositor), 0.301 (DCC) 
• R-Value Work:  0.264 (Depositor), 0.266 (DCC) 
• R-Value Observed: 0.266 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.53	α = 90
b = 72.7	β = 96.16
c = 70.18	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-05-01 
Deposition Author(s): Sorrentino, L., Cossu, F., Milani, M., Mastrangelo, E.

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Funding Organization	Location	Grant Number
Italian Association for Cancer Research	Italy	17083

Revision History  

• Version 1.0: 2019-05-01
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description