6O81

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • 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 an ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit epsilon AB721Homo sapiensMutation(s): 0 
Gene Names: EIF2B5EIF2BE
Find proteins for Q13144 (Homo sapiens)
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PHAROS:  Q13144
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit beta CD368Homo sapiensMutation(s): 0 
Gene Names: EIF2B2EIF2BB
Find proteins for P49770 (Homo sapiens)
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PHAROS:  P49770
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit delta EF523Homo sapiensMutation(s): 0 
Gene Names: EIF2B4EIF2BD
Find proteins for Q9UI10 (Homo sapiens)
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PHAROS:  Q9UI10
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit alpha GH305Homo sapiensMutation(s): 0 
Gene Names: EIF2B1EIF2BA
Find proteins for Q14232 (Homo sapiens)
Explore Q14232 
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PHAROS:  Q14232
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit gamma IJ452Homo sapiensMutation(s): 0 
Gene Names: EIF2B3
Find proteins for Q9NR50 (Homo sapiens)
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PHAROS:  Q9NR50
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 1 LM315Homo sapiensMutation(s): 0 
Gene Names: EIF2S1EIF2A
Find proteins for P05198 (Homo sapiens)
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PHAROS:  P05198
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 3 ST472Homo sapiensMutation(s): 0 
Gene Names: EIF2S3EIF2G
EC: 3.6.5.3
Find proteins for P41091 (Homo sapiens)
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PHAROS:  P41091
Protein Feature View
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor eiF2 beta-subunit de14Homo sapiensMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C7B
Query on C7B

Download Ideal Coordinates CCD File 
C
2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy)ethanoylamino]cyclohexyl]ethanamide
C22 H24 Cl2 N2 O4
HJGMCDHQPXTGAV-IYARVYRRSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States55108523

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