7BMK | pdb_00007bmk

ATP-Competitive Partial Antagonists-'PAIR's-Rheostatically Modulate IRE1alpha's Kinase Helix-alphaC to Segregate its RNase-Mediated Biological Outputs

• PDB DOI: https://doi.org/10.2210/pdb7BMK/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2021-01-20 Released: 2021-09-29 
• Deposition Author(s): Feldman, H.C., Ghosh, R., Auyeung, V., Mueller, J.L., Vidadala, V.N., Olivier, A., Backes, B.J., Zikherman, J., Papa, F.R., Maly, D.J.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.235 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

ATP-competitive partial antagonists of the IRE1 alpha RNase segregate outputs of the UPR.

Feldman, H.C., Ghosh, R., Auyeung, V.C., Mueller, J.L., Kim, J.H., Potter, Z.E., Vidadala, V.N., Perera, B.G.K., Olivier, A., Backes, B.J., Zikherman, J., Papa, F.R., Maly, D.J.

(2021) Nat Chem Biol 17: 1148-1156

• PubMed: 34556859 
• DOI: https://doi.org/10.1038/s41589-021-00852-0
• Primary Citation Related Structures: 
  7BMK


• PubMed Abstract: 
  

  The unfolded protein response (UPR) homeostatically matches endoplasmic reticulum (ER) protein-folding capacity to cellular secretory needs. However, under high or chronic ER stress, the UPR triggers apoptosis. This cell fate dichotomy is promoted by differential activation of the ER transmembrane kinase/endoribonuclease (RNase) IRE1α. We previously found that the RNase of IRE1α can be either fully activated or inactivated by ATP-competitive kinase inhibitors. Here we developed kinase inhibitors, partial antagonists of IRE1α RNase (PAIRs), that partially antagonize the IRE1α RNase at full occupancy. Biochemical and structural studies show that PAIRs promote partial RNase antagonism by intermediately displacing the helix αC in the IRE1α kinase domain. In insulin-producing β-cells, PAIRs permit adaptive splicing of Xbp1 mRNA while quelling destructive ER mRNA endonucleolytic decay and apoptosis. By preserving Xbp1 mRNA splicing, PAIRs allow B cells to differentiate into immunoglobulin-producing plasma cells. Thus, an intermediate RNase-inhibitory 'sweet spot', achieved by PAIR-bound IRE1α, captures a desirable conformation for drugging this master UPR sensor/effector.

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Organizational Affiliation: 
• Department of Chemistry, University of Washington, Seattle, WA, USA.
Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
Lung Biology Center, University of California, San Francisco, San Francisco, CA, USA.
Department of Pathology, University of California, San Francisco, San Francisco, CA, USA.
Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.
Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA.
Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, University of California, San Francisco, San Francisco, CA, USA.
Department of Medicine, University of California, San Francisco, San Francisco, CA, USA. [e-mail].
Lung Biology Center, University of California, San Francisco, San Francisco, CA, USA. [e-mail].
Department of Pathology, University of California, San Francisco, San Francisco, CA, USA. [e-mail].
Diabetes Center, University of California, San Francisco, San Francisco, CA, USA. [e-mail].
Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA. [e-mail].
Department of Chemistry, University of Washington, Seattle, WA, USA. [e-mail].
Department of Biochemistry, University of Washington, Seattle, WA, USA. [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 102.92 kDa 
• Atom Count: 7,573 
• Modeled Residue Count: 798 
• Deposited Residue Count: 868 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase/endoribonuclease IRE1	A, B	434	Homo sapiens	Mutation(s): 0  Gene Names: ERN1, IRE1 EC: 2.7.11.1 (PDB Primary Data), 3.1.26 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O75460 (Homo sapiens) Explore O75460  Go to UniProtKB:  O75460
PHAROS:  O75460 GTEx:  ENSG00000178607

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U4N	C [auth A], X [auth B]	2,2,2-tris(fluoranyl)-~{N}-[4-[3-[2-[[(3~{S})-piperidin-3-yl]amino]pyrimidin-4-yl]pyridin-2-yl]oxynaphthalen-1-yl]ethanesulfonamide C26 H25 F3 N6 O3 S LVBYPSVRFGNRPW-KRWDZBQOSA-N
PGE	DA [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	AA [auth B], CA [auth B], FA [auth B], W [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	BA [auth B], D [auth A], E [auth A], F [auth A], I [auth A], K [auth A], L [auth A], R [auth A], S [auth A], Y [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	EA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], IA [auth B], J [auth A], JA [auth B], KA [auth B], LA [auth B], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], T [auth A], U [auth A], V [auth A], Z [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.235 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.903	α = 90
b = 72.813	β = 129.82
c = 119.239	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-09-29 
Deposition Author(s): Feldman, H.C., Ghosh, R., Auyeung, V., Mueller, J.L., Vidadala, V.N., Olivier, A., Backes, B.J., Zikherman, J., Papa, F.R., Maly, D.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R01DK100623
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	U01DK123609

Revision History  

• Version 1.0: 2021-09-29
  Type: Initial release
  
• Version 1.1: 2022-04-13
  Changes: Database references
• Version 1.2: 2024-06-19
  Changes: Data collection, Refinement description