6EZO

Eukaryotic initiation factor EIF2B in complex with ISRIB

• PDB DOI:  https://doi.org/10.2210/pdb6EZO/pdb
• EM Map EMD-4162: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2017-11-16 Released: 2018-03-28 
• Deposition Author(s): Faille, A., Weis, F., Zyryanova, A., Warren, A.J., Ron, D.
• Funding Organization(s): Wellcome Trust, Medical Research Council (United Kingdom)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Binding of ISRIB reveals a regulatory site in the nucleotide exchange factor eIF2B.

Zyryanova, A.F., Weis, F., Faille, A., Alard, A.A., Crespillo-Casado, A., Sekine, Y., Harding, H.P., Allen, F., Parts, L., Fromont, C., Fischer, P.M., Warren, A.J., Ron, D.

(2018) Science 359: 1533-1536

• PubMed: 29599245 
• DOI: https://doi.org/10.1126/science.aar5129
• Primary Citation of Related Structures:  
  6EZO


• PubMed Abstract: 
  

The integrated stress response (ISR) is a conserved translational and transcriptional program affecting metabolism, memory, and immunity. The ISR is mediated by stress-induced phosphorylation of eukaryotic translation initiation factor 2α (eIF2α) that attenuates the guanine nucleotide exchange factor eIF2B. A chemical inhibitor of the ISR, ISRIB, reverses the attenuation of eIF2B by phosphorylated eIF2α, protecting mice from neurodegeneration and traumatic brain injury. We describe a 4.1-angstrom-resolution cryo-electron microscopy structure of human eIF2B with an ISRIB molecule bound at the interface between the β and δ regulatory subunits. Mutagenesis of residues lining this pocket altered the hierarchical cellular response to ISRIB analogs in vivo and ISRIB binding in vitro. Our findings point to a site in eIF2B that can be exploited by ISRIB to regulate translation.

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Organizational Affiliation: 

Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK. [e-mail] [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 10-mer - A6B4 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 528.3 kDa 
• Atom Count: 18,758 
• Modelled Residue Count: 3,367 
• Deposited Residue Count: 4,748 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor eIF-2B subunit alpha	A, B	305	Homo sapiens	Mutation(s): 0  Gene Names: EIF2B1, EIF2BA
UniProt & NIH Common Fund Data Resources
Find proteins for Q14232 (Homo sapiens) Explore Q14232  Go to UniProtKB:  Q14232
PHAROS:  Q14232

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor eIF-2B subunit beta	C, D	373	Homo sapiens	Mutation(s): 0  Gene Names: EIF2B2, EIF2BB
UniProt & NIH Common Fund Data Resources
Find proteins for P49770 (Homo sapiens) Explore P49770  Go to UniProtKB:  P49770
PHAROS:  P49770

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor eIF-2B subunit gamma	E, F	452	Homo sapiens	Mutation(s): 0  Gene Names: EIF2B3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NR50 (Homo sapiens) Explore Q9NR50  Go to UniProtKB:  Q9NR50
PHAROS:  Q9NR50

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor eIF-2B subunit delta	G, H	523	Homo sapiens	Mutation(s): 0  Gene Names: EIF2B4, EIF2BD
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UI10 (Homo sapiens) Explore Q9UI10  Go to UniProtKB:  Q9UI10
PHAROS:  Q9UI10

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Human eukaryotic initiation factor EIF2B epsilon subunits	I, J	721	Homo sapiens	Mutation(s): 0  Gene Names: EIF2B5, EIF2BE
UniProt & NIH Common Fund Data Resources
Find proteins for Q13144 (Homo sapiens) Explore Q13144  Go to UniProtKB:  Q13144
PHAROS:  Q13144

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C7B	K [auth D]	2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy)ethanoylamino]cyclohexyl]ethanamide C22 H24 Cl2 N2 O4 HJGMCDHQPXTGAV-IYARVYRRSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	REFMAC
RECONSTRUCTION	RELION

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-03-28 
Deposition Author(s): Faille, A., Weis, F., Zyryanova, A., Warren, A.J., Ron, D.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	WT200848/Z/16/Z
Medical Research Council (United Kingdom)	United Kingdom	RG67621

Revision History  

• Version 1.0: 2018-03-28
  Type: Initial release
  
• Version 1.1: 2018-04-04
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2018-04-11
  Changes: Data collection, Database references
• Version 1.3: 2018-10-17
  Changes: Data collection, Refinement description
• Version 1.4: 2019-12-11
  Changes: Other, Structure summary