6JLZ

P-eIF2a - eIF2B complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

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

  • 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 ...

    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.


    Organizational Affiliation

    RIKEN Center for Biosystems Dynamics Research, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. takuhiro.ito@riken.jp.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit alphaA, B341Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: tif221SPCC11E10.07c
UniProt
Find proteins for Q9USP0 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Probable translation initiation factor eIF-2B subunit betaC, D399Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: tif222SPAC343.14c
UniProt
Find proteins for Q9UT76 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Probable translation initiation factor eIF-2B subunit gammaE, F458Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: tif223SPAC4D7.09
UniProt
Find proteins for P56288 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Probable translation initiation factor eIF-2B subunit deltaG, H467Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: tif224SPAC21E11.06
UniProt
Find proteins for Q09924 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Probable translation initiation factor eIF-2B subunit epsilonI, J678Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: tif225SPAC8C9.15c
UniProt
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit alphaK [auth L], L [auth M]304Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SUI2TIF211YJR007WJ1429
UniProt
Find proteins for P20459 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
K [auth L], L [auth M]L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.578α = 90
b = 207.712β = 96.96
c = 155.744γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-03-07 
  • Released Date: 2019-05-01 
  • Deposition Author(s): Kashiwagi, K., Ito, T.

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan--
Japan Agency for Medical Research and Development (AMED)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-01
    Type: Initial release
  • Version 1.1: 2019-05-15
    Changes: Data collection, Database references