Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 14-mer - A2B2C2D2E2F1G1H1I1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 14-mer - A6B4C1D1E1F1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 684.36 kDa 
• Atom Count: 32731 
• Residue Count: 4264 
• Unique protein chains: 8

6K72

eIF2(aP) - eIF2B complex

• DOI: 10.2210/pdb6K72/pdb
• Entry: 6K72 supersedes: 6JLX
• EMDataResource: EMD-9841

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


• Deposited: 2019-06-05 Released: 2019-07-10 
• Deposition Author(s): Kashiwagi, K., Yokoyama, T., Ito, T.
• Funding Organization(s): Japan Society for the Promotion of Science, Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for eIF2B inhibition in integrated stress response.

Kashiwagi, K., Yokoyama, T., Nishimoto, M., Takahashi, M., Sakamoto, A., Yonemochi, M., Shirouzu, M., Ito, T.

(2019) Science 364: 495-499

• PubMed: 31048492 
• DOI: 10.1126/science.aaw4104
• Primary Citation of Related Structures:  
  6JLY, 6JLZ, 6K72, 6K71


• PubMed Abstract: 
  

A core event in the integrated stress response, an adaptive pathway common to all eukaryotic cells in response to various stress stimuli, is the phosphorylation of eukaryotic translation initiation factor 2 (eIF2). Normally, unphosphorylated eIF2 transfers the methionylated initiator tRNA to the ribosome in a guanosine 5'-triphosphate-dependent manner. By contrast, phosphorylated eIF2 inhibits its specific guanine nucleotide exchange factor, eIF2B. To elucidate how the eIF2 phosphorylation status regulates the eIF2B activity, we determined cryo-electron microscopic and crystallographic structures of eIF2B in complex with unphosphorylated or phosphorylated eIF2. The unphosphorylated and phosphorylated forms of eIF2 bind to eIF2B in completely different manners: the nucleotide exchange-active and -inactive modes, respectively. These structures explain how phosphorylated eIF2 dominantly inhibits the nucleotide exchange activity of eIF2B.

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Organizational Affiliation: 

RIKEN Center for Biosystems Dynamics Research, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. [e-mail].

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
Find proteins for Q14232 (Homo sapiens) Explore Q14232  Go to UniProtKB:  Q14232
NIH Common Fund Data Resources
PHAROS:  Q14232 GTEx:  ENSG00000111361

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor eIF-2B subunit beta	C, D	351	Homo sapiens	Mutation(s): 0  Gene Names: EIF2B2, EIF2BB
Find proteins for P49770 (Homo sapiens) Explore P49770  Go to UniProtKB:  P49770
NIH Common Fund Data Resources
PHAROS:  P49770 GTEx:  ENSG00000119718

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
Find proteins for Q9NR50 (Homo sapiens) Explore Q9NR50  Go to UniProtKB:  Q9NR50
NIH Common Fund Data Resources
PHAROS:  Q9NR50 GTEx:  ENSG00000070785

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
Find proteins for Q9UI10 (Homo sapiens) Explore Q9UI10  Go to UniProtKB:  Q9UI10
NIH Common Fund Data Resources
PHAROS:  Q9UI10 GTEx:  ENSG00000115211

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor eIF-2B subunit epsilon	I, J	721	Homo sapiens	Mutation(s): 0  Gene Names: EIF2B5, EIF2BE
Find proteins for Q13144 (Homo sapiens) Explore Q13144  Go to UniProtKB:  Q13144
NIH Common Fund Data Resources
PHAROS:  Q13144 GTEx:  ENSG00000145191

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 2 subunit 1	K, L	315	Homo sapiens	Mutation(s): 0  Gene Names: EIF2S1, EIF2A
Find proteins for P05198 (Homo sapiens) Explore P05198  Go to UniProtKB:  P05198
NIH Common Fund Data Resources
PHAROS:  P05198 GTEx:  ENSG00000134001

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 2 subunit 2	M	333	Homo sapiens	Mutation(s): 0  Gene Names: EIF2S2, EIF2B
Find proteins for P20042 (Homo sapiens) Explore P20042  Go to UniProtKB:  P20042
NIH Common Fund Data Resources
PHAROS:  P20042 GTEx:  ENSG00000125977

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 2 subunit 3	P	472	Homo sapiens	Mutation(s): 0  Gene Names: EIF2S3, EIF2G EC: 3.6.5.3
Find proteins for P41091 (Homo sapiens) Explore P41091  Go to UniProtKB:  P41091
NIH Common Fund Data Resources
PHAROS:  P41091 GTEx:  ENSG00000130741

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-06-05 
• Released Date: 2019-07-10 
Deposition Author(s): Kashiwagi, K., Yokoyama, T., Ito, T.
• This entry supersedes: 6JLX

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	--
Japan Agency for Medical Research and Development (AMED)	Japan	--

Revision History 

• Version 1.0: 2019-07-10
  Type: Initial release
  
• Version 1.1: 2019-11-06
  Changes: Data collection, Other