Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 13-mer - A2B2C2D2E1F1G1H1I1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 13-mer - A6B2C2D1E1F1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 615.22 kDa 
• Atom Count: 28576 
• Modelled Residue Count: 4114 
• Deposited Residue Count: 5538 
• Unique protein chains: 8

6O85

Electron cryo-microscopy of the eukaryotic translation initiation factor 2B bound to eukaryotic translation initiation factor 2 from Homo sapiens

• DOI: 10.2210/pdb6O85/pdb
• EMDataResource: EMD-0651

• Classification: TRANSLATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-03-08 Released: 2019-05-15 
• Deposition Author(s): Nguyen, H.C., Kenner, L.R., Frost, A.S.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.03 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

eIF2B-catalyzed nucleotide exchange and phosphoregulation by the integrated stress response.

Kenner, L.R., Anand, A.A., Nguyen, H.C., Myasnikov, A.G., Klose, C.J., McGeever, L.A., Tsai, J.C., Miller-Vedam, L.E., Walter, P., Frost, A.

(2019) Science 364: 491-495

• PubMed: 31048491 
• DOI: 10.1126/science.aaw2922
• Primary Citation of Related Structures:  
  6O81, 6O85, 6O9Z


• PubMed Abstract: 
  

The integrated stress response (ISR) tunes the rate of protein synthesis. Control is exerted by phosphorylation of the general translation initiation factor eIF2. eIF2 is a guanosine triphosphatase that becomes activated by eIF2B, a two-fold symmetric and heterodecameric complex that functions as eIF2's dedicated nucleotide exchange factor. Phosphorylation converts eIF2 from a substrate into an inhibitor of eIF2B. We report cryo-electron microscopy structures of eIF2 bound to eIF2B in the dephosphorylated state. The structures reveal that the eIF2B decamer is a static platform upon which one or two flexible eIF2 trimers bind and align with eIF2B's bipartite catalytic centers to catalyze nucleotide exchange. Phosphorylation refolds eIF2α, allowing it to contact eIF2B at a different interface and, we surmise, thereby sequestering it into a nonproductive complex.

---

Organizational Affiliation: 

Chan Zuckerberg Biohub, San Francisco, CA, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor eIF-2B subunit epsilon	A, B	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 GTEx:  ENSG00000145191

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor eIF-2B subunit beta	C, D	368	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 GTEx:  ENSG00000119718

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor eIF-2B subunit delta	E, F	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 GTEx:  ENSG00000115211

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor eIF-2B subunit alpha	G, H	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 GTEx:  ENSG00000111361

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor eIF-2B subunit gamma	I, J	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 GTEx:  ENSG00000070785

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 2 subunit 1	K [auth L]	314	Homo sapiens	Mutation(s): 0  Gene Names: EIF2S1, EIF2A
UniProt & NIH Common Fund Data Resources
Find proteins for P05198 (Homo sapiens) Explore P05198  Go to UniProtKB:  P05198
PHAROS:  P05198 GTEx:  ENSG00000134001

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 2 subunit 3	L [auth S]	472	Homo sapiens	Mutation(s): 0  Gene Names: EIF2S3, EIF2G EC: 3.6.5.3
UniProt & NIH Common Fund Data Resources
Find proteins for P41091 (Homo sapiens) Explore P41091  Go to UniProtKB:  P41091
PHAROS:  P41091 GTEx:  ENSG00000130741

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 2 subunit beta	M [auth d]	14	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C7B (Subject of Investigation/LOI)	N [auth C]	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: 3.03 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-03-08 
• Released Date: 2019-05-15 
Deposition Author(s): Nguyen, H.C., Kenner, L.R., Frost, A.S.

---

Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	55108523

Revision History  

• Version 1.0: 2019-05-15
  Type: Initial release
  
• Version 1.1: 2019-11-20
  Changes: Author supporting evidence, Structure summary
• Version 1.2: 2019-12-18
  Changes: Other